Substance files get automatically deleted/re-added using Unity VCS

Hey all, have a bit of an odd issue that I'm hoping you can help with.  Our team is using Unity VCS for source control, but we have a frequent issue of files in the Substance Unity plugin showing as deleted and needing to re-add them.  For example, Substance was working fine then I pulled in changes from a coworker (who hadn't touched the Substance plugin) and a bunch of the plugin files got deleted.

The solution is to re-import the plugin, but now my version control is showing me as having added a bunch of plugin files, where nowhere in the project history do they show as being deleted.  It's not a huge dealbreaker having to re-import the plugin when you pull in changes, but it's odd that it only happens with the Substance plugin.  It's also happened across several projects with different coworkers.

Are you aware of any issue like this?  Any suggestions how to fix it?