To make sure that your comments are preserved you can't use anything that would make them auto-update.
For example this includes:
- Increasing/decreasing the font size with the keyboard short cut
- Installing or uninstalling a package with Package Control
- Changing colors through the menu
- Using SublimeLinter (it makes modified version of themes and switches to them)
So basically, I would say that it is not worth it to try to preserve them, but it is up to you. Just remember that you will basically not be able to use Package Control or any of several other packages or even some built in options.