My concern is when I leave one VectorStyler file open as a reference while copying elements or information into another document. If I accidentally move, delete, paste, or change something in the reference file, Auto Save could overwrite the original before I notice. I understand I can set the timer for up to 20 min, but sometimes I forget to close out a reference file because it's out of sight-out of mind

A per-document option would solve this. Possible implementations could include:

Disable Auto Save for the current document
Open document as read-only
Lock document against saving
Warn before Auto Save overwrites a file that was opened as a reference
Add an “Open as Reference” option

The ideal workflow would let Auto Save remain enabled globally while protecting selected files from accidental changes.

My personal preference would be an option to open a document as "read-only"
A possible location is right ehre in the file menu

This would be especially useful when working with templates, client-approved artwork, production files, or older designs that need to remain unchanged.

I would also feel safer with these options, knowing it's far less likely to accidentally save over a file I left open by mistake or that I need to keep track of how long its open for fear it gets saved over.