Could WPMUDEV have removed Thrive content builder?

I installed the wpmudev dashboard and a few of the plugins on 2 of my sites to test them out. on both of those sites several of my plugins from thrive themes have disappeared!

I'm suspecting Defender might have caused it,

my questions are:

1 - could WPMUDEV have removed my plugins?
2 - considering these are newer sites I'm working on, without backups, how can I restore them?

what i've tried
1 - I've tried deactivating all wpmudev plugins, that didn't fix it.
2 - I also tried to reinstall the thrive plugins, but it said the file folder already existed or something like that.