After using a report trojan on one fabricator, a different fabricator that i didn't know about completed an Enhanced Nova Cannon.
This added both a comment and a Fabricator intel marker, but turned off machine intel at the same time.
Here's a video of it :
https://imgur.com/a/machine-intel-turns-off-BVDFbfz
You can see that there was no Fabricator intel marker in the direction of the report comment, meaning i didn't know about it,
and also that my other intel (Prototype Stockpile) was not deactivated along with general machine intel.
There are indeed at least a couple new ways it can accidentally get turned off, haven't gotten a full list of them yet but noticed it myself during play, will add this to the list to check!
Three hours! That's how long it took to properly track and fix this considering how unusual the conditions ended up being xD
Good timing on this at least, since I normally don't use this particular hack so never really had a chance to encounter it, but saw it a lot during my stream and realized while fixing this that it was due to a new Beta 15 feature that automatically adds machine intel for those within terrain revealed through other means such as Layout(Zone), which is something I do a lot and that's why I was confused my intel kept turn off in my recent stream :P (this would've started happening to a lot more people if it went public with Beta 15 without the fix...)