This is a known issue. There are other threads about it.
Perhaps use “automations2” etc if you want to them up manually and leave the automations.yaml to UI setup.
This is not a Blueprint question, and this is not an issue, it is the way Home Assistant works.
The automation file is parsed, interpreted, deleted, and re-written every time you use the HA tools like the GUI editor, open a BP, reload automations, all that stuff. Same with scripts. If you want to save all the comments and visual formatting, you have to save automations and scripts in other files and split your automations up.
Packages are another way to do it.