So oddly enough, I added the logger, then enabled the services again and saw that both thermostats have devices and are functioning. I restarted Home Assistant again just to check and then saw that my second thermostat retains the device and entities but now all unavailable. Looking at the logs, possible it has to do with the NACK?
The first thermostat still has all the entities and is functional
2023-03-15 16:07:08.442 DEBUG (MainThread) [custom_components.aprilaire] Manually updated aprilaire data
2023-03-15 16:07:08.457 DEBUG (MainThread) [custom_components.aprilaire] Manually updated aprilaire data
2023-03-15 16:07:08.457 DEBUG (MainThread) [custom_components.aprilaire] Manually updated aprilaire data
2023-03-15 16:07:08.506 INFO (MainThread) [custom_components.aprilaire] Aprilaire connection made
2023-03-15 16:07:08.508 DEBUG (MainThread) [custom_components.aprilaire] Manually updated aprilaire data
2023-03-15 16:07:10.508 DEBUG (MainThread) [custom_components.aprilaire] Queuing data, sequence=1, action=Action.READ_REQUEST, functional_domain=FunctionalDomain.IDENTIFICATION, attribute=2
2023-03-15 16:07:10.508 DEBUG (MainThread) [custom_components.aprilaire] Queuing data, sequence=2, action=Action.READ_REQUEST, functional_domain=FunctionalDomain.CONTROL, attribute=7
2023-03-15 16:07:10.509 DEBUG (MainThread) [custom_components.aprilaire] Queuing data, sequence=3, action=Action.READ_REQUEST, functional_domain=FunctionalDomain.CONTROL, attribute=1
2023-03-15 16:07:10.509 DEBUG (MainThread) [custom_components.aprilaire] Queuing data, sequence=4, action=Action.READ_REQUEST, functional_domain=FunctionalDomain.SENSORS, attribute=2
2023-03-15 16:07:10.509 DEBUG (MainThread) [custom_components.aprilaire] Queuing data, sequence=5, action=Action.READ_REQUEST, functional_domain=FunctionalDomain.IDENTIFICATION, attribute=5
2023-03-15 16:07:10.509 DEBUG (MainThread) [custom_components.aprilaire] Queuing data, sequence=6, action=Action.WRITE, functional_domain=FunctionalDomain.STATUS, attribute=1
2023-03-15 16:07:10.509 DEBUG (MainThread) [custom_components.aprilaire] Queuing data, sequence=7, action=Action.WRITE, functional_domain=FunctionalDomain.STATUS, attribute=2
2023-03-15 16:07:10.513 INFO (MainThread) [custom_components.aprilaire] Sent data: 01 01 00 03 02 08 02 fb
2023-03-15 16:07:10.514 INFO (MainThread) [custom_components.aprilaire] Sent data: 01 02 00 03 02 02 07 19
2023-03-15 16:07:10.514 INFO (MainThread) [custom_components.aprilaire] Sent data: 01 03 00 03 02 02 01 e8
2023-03-15 16:07:10.515 INFO (MainThread) [custom_components.aprilaire] Sent data: 01 04 00 03 02 05 02 81
2023-03-15 16:07:10.515 INFO (MainThread) [custom_components.aprilaire] Sent data: 01 05 00 03 02 08 05 01
2023-03-15 16:07:10.516 INFO (MainThread) [custom_components.aprilaire] Sent data: 01 06 00 20 01 07 01 01 00 00 00 00 01 00 00 00 00 01 00 00 00 01 00 00 00 00 00 01 00 01 00 01 01 01 00 00 6f
2023-03-15 16:07:10.517 INFO (MainThread) [custom_components.aprilaire] Sent data: 01 07 00 04 01 07 02 01 3b
2023-03-15 16:07:10.520 INFO (MainThread) [custom_components.aprilaire] Aprilaire data received 01 03 00 02 06 03 96
2023-03-15 16:07:10.520 DEBUG (MainThread) [custom_components.aprilaire] Received data, action=Action.NACK, functional_domain=FunctionalDomain.NACK, attribute=0
2023-03-15 16:07:10.520 ERROR (MainThread) [custom_components.aprilaire] Received NACK for attribute 3
2023-03-15 16:07:10.522 INFO (MainThread) [custom_components.aprilaire] Aprilaire data received 01 04 00 02 06 03 cd 01 01 00 11 03 08 02 b4 82 55 50 93 6d 01 49 02 01 02 0d 04 0e 51
2023-03-15 16:07:10.522 DEBUG (MainThread) [custom_components.aprilaire] Received data, action=Action.NACK, functional_domain=FunctionalDomain.NACK, attribute=0
2023-03-15 16:07:10.522 ERROR (MainThread) [custom_components.aprilaire] Received NACK for attribute 3
2023-03-15 16:07:10.524 INFO (MainThread) [custom_components.aprilaire] Aprilaire data received 01 02 00 08 03 02 07 04 01 00 00 00 ef
2023-03-15 16:07:10.524 DEBUG (MainThread) [custom_components.aprilaire] Received data, action=Action.READ_RESPONSE, functional_domain=FunctionalDomain.CONTROL, attribute=7
2023-03-15 16:07:10.524 DEBUG (MainThread) [custom_components.aprilaire] Manually updated aprilaire data
2023-03-15 16:07:10.529 INFO (MainThread) [custom_components.aprilaire] Aprilaire data received 01 80 00 2f 05 01 01 01 01 00 00 00 00 00 01 00 00 04 05 00 01 00 00 00 00 01 02 02 04 00 03 00 00 00 00 00 02 00 3d 51 00 0d 01 01 01 00 00 00 0d 0d 00 d3
2023-03-15 16:07:10.530 DEBUG (MainThread) [custom_components.aprilaire] Received data, action=Action.COS, functional_domain=FunctionalDomain.SETUP, attribute=1
2023-03-15 16:07:10.530 DEBUG (MainThread) [custom_components.aprilaire] Manually updated aprilaire data
2023-03-15 16:07:10.530 INFO (MainThread) [custom_components.aprilaire] Aprilaire data received 01 80 00 07 05 02 01 03 03 18 55 bc
2023-03-15 16:07:10.530 DEBUG (MainThread) [custom_components.aprilaire] Received data, action=Action.COS, functional_domain=FunctionalDomain.CONTROL, attribute=1
2023-03-15 16:07:10.531 DEBUG (MainThread) [custom_components.aprilaire] Manually updated aprilaire data
2023-03-15 16:07:10.533 INFO (MainThread) [custom_components.aprilaire] Aprilaire data received 01 80 00 08 05 02 07 04 01 00 00 00 3e
2023-03-15 16:07:10.534 DEBUG (MainThread) [custom_components.aprilaire] Received data, action=Action.COS, functional_domain=FunctionalDomain.CONTROL, attribute=7
2023-03-15 16:07:10.534 DEBUG (MainThread) [custom_components.aprilaire] Manually updated aprilaire data
2023-03-15 16:07:10.534 INFO (MainThread) [custom_components.aprilaire] Aprilaire data received 01 80 00 0d 05 03 04 01 03 18 55 ff 1e 13 0f 03 17 ff
2023-03-15 16:07:10.535 DEBUG (MainThread) [custom_components.aprilaire] Received data, action=Action.COS, functional_domain=FunctionalDomain.SCHEDULING, attribute=4
2023-03-15 16:07:10.535 DEBUG (MainThread) [custom_components.aprilaire] Manually updated aprilaire data
2023-03-15 16:07:10.537 INFO (MainThread) [custom_components.aprilaire] Aprilaire data received 01 80 00 0b 05 05 02 00 55 03 92 04 00 03 00 f6
2023-03-15 16:07:10.537 DEBUG (MainThread) [custom_components.aprilaire] Received data, action=Action.COS, functional_domain=FunctionalDomain.SENSORS, attribute=2
2023-03-15 16:07:10.538 DEBUG (MainThread) [custom_components.aprilaire] Manually updated aprilaire data
2023-03-15 16:07:10.539 INFO (MainThread) [custom_components.aprilaire] Aprilaire data received 01 80 00 07 05 07 06 00 00 00 00 59 01 80 00 07 05 07 07 00 00 00 00 8a
2023-03-15 16:07:10.539 DEBUG (MainThread) [custom_components.aprilaire] Received data, action=Action.COS, functional_domain=FunctionalDomain.STATUS, attribute=6
2023-03-15 16:07:10.539 DEBUG (MainThread) [custom_components.aprilaire] Received data, action=Action.COS, functional_domain=FunctionalDomain.STATUS, attribute=7
2023-03-15 16:07:10.539 DEBUG (MainThread) [custom_components.aprilaire] Manually updated aprilaire data
2023-03-15 16:07:10.539 DEBUG (MainThread) [custom_components.aprilaire] Manually updated aprilaire data
2023-03-15 16:07:10.541 INFO (MainThread) [custom_components.aprilaire] Aprilaire data received 01 80 00 0a 05 08 01 49 02 01 02 0d 04 0e b0
2023-03-15 16:07:10.541 DEBUG (MainThread) [custom_components.aprilaire] Received data, action=Action.COS, functional_domain=FunctionalDomain.IDENTIFICATION, attribute=1
2023-03-15 16:07:10.542 DEBUG (MainThread) [custom_components.aprilaire] Manually updated aprilaire data
2023-03-15 16:07:10.542 INFO (MainThread) [custom_components.aprilaire] Aprilaire data received 01 80 00 04 05 07 08 00 ab 01 80 00 04 05 07 02 01 74
2023-03-15 16:07:10.542 DEBUG (MainThread) [custom_components.aprilaire] Received data, action=Action.COS, functional_domain=FunctionalDomain.STATUS, attribute=8
2023-03-15 16:07:10.542 DEBUG (MainThread) [custom_components.aprilaire] Received data, action=Action.COS, functional_domain=FunctionalDomain.STATUS, attribute=2
2023-03-15 16:07:10.542 DEBUG (MainThread) [custom_components.aprilaire] Manually updated aprilaire data
2023-03-15 16:07:10.542 DEBUG (MainThread) [custom_components.aprilaire] Manually updated aprilaire data