Weird issues for 2+ days

My HA has been a mess for three days I don’t know where to start. I use SmartThings to talk to my devices on zwave and zigbee. Sunday I installed a couple Inovelli black dimmers without excluding the black series switch devices I removed. About the same time, HA started acting very weird. So what is weird?

1 - When I go to integrations, various ones will report being ‘not loaded’. Tuya, Plex, SmartThings have all done this.

2 - on the Supervisor page, some installed add-ons are not listed some time and show loaded at others Mosquito Broker is the one I notice

3 - Lovelace pages load without status, then refresh and might have status. Or, they load with status, then refresh all greyed out.
3.5 Web pages refresh randomly - even on Firfox

4 - Various integrations aren’t displaying the reload option. SmartThings being the one I notice most.

5 - the iOS app displayed an SSL error and wouldn’t connect for two days. (working now)

6 - Supervisor kept switching from showing I was running core v21.4.3 to 21.4.6.

7 - Configuration.yaml entries went missing
8 - many automations just stopped working. (motion based/time based)

Details: Running core 21.4.6, supervisor 21.4.0, running HA OS 5.13 in a VM

VM disk is 35% usage. htop in the terminal says HA is using 1.1GB of 1.9GB

What I’ve done: Restored a Saturday full backup on Monday; restarted SmartThings; reinstalled the original switches (only due to an incompatibility with the LED lights I was hoping to control)

I’m at a lost on what to do next.

Here are recent log entries showing the many things not working well:

Updating tuya light took longer than the scheduled update interval 0:00:15
8:51:04 PM – (WARNING) Light - message first occurred at 9:34:59 AM and shows up 734 times
Updating device list from legacy took longer than the scheduled scan interval 0:00:10
8:50:57 PM – (WARNING) Device tracker - message first occurred at 8:27:28 AM and shows up 1041 times
Unexpectedly disconnected from Roomba, code Bad protocol
8:50:54 PM – (WARNING) /usr/local/lib/python3.8/site-packages/roombapy/ - message first occurred at 8:24:53 AM and shows up 689 times
Timeout fetching MartinOrbi (Gateway) data
8:50:51 PM – (ERROR) UPnP - message first occurred at 8:23:52 AM and shows up 236 times
Updating tplink switch took longer than the scheduled update interval 0:00:30
8:50:38 PM – (WARNING) switch - message first occurred at 8:29:27 AM and shows up 38 times
Error fetching roku data: Invalid response from API: Timeout occurred while connecting to device
8:50:18 PM – (ERROR) Roku - message first occurred at 8:23:47 AM and shows up 631 times
Error scanning devices
8:50:17 PM – (WARNING) netgear - message first occurred at 8:27:48 AM and shows up 293 times
Error talking to API
8:50:17 PM – (ERROR) /usr/local/lib/python3.8/site-packages/pynetgear/ - message first occurred at 8:27:48 AM and shows up 277 times
Update of switch.tree_2 is taking over 10 seconds
8:49:48 PM – (WARNING) helpers/ - message first occurred at 8:28:07 AM and shows up 144 times
Could not connect to Plex server: HDA PLex (HTTPSConnectionPool(host='', port=443): Read timed out. (read timeout=30))
8:43:01 PM – (ERROR) Plex Media Server - message first occurred at 8:26:44 AM and shows up 166 times
Websocket connection failed, retrying in 15s: Cannot connect to host ssl:default [Try again]
8:42:45 PM – (ERROR) /usr/local/lib/python3.8/site-packages/ - message first occurred at 8:28:12 AM and shows up 122 times

This is embarrassing. I recently moved my VBox VM from Debian to Windows to solve an issue where time-based automations weren’t firing. Well, I didn’t properly disable autostart on the the vm I left behind. It restarted - both were running.
I’m an idiot.