Widgets deactivated unexpectedly

I am aware that widgets may be deactivated when changing themes. However, I have faced issues where widgets are deactivated when no apparent administrative task is being performed or, perhaps, when a plugin that should be completely unrelated to the widgets is updated. I am pretty sure that no malicious software is running on my site.

So, I am asking for two bits of help:
1) where, precisely, is the code that deactivates a widget (file, function name)
2) any suggestions for troubleshooting this issue? My theme vendor does not seem to think it is their problem. I don’t know how to start figuring this out, especially when no obvious changes can be correlated with the deactivation.