This is a serious problem, especially for folks with big mod lists. In addition to all the complaints mentioned in this thread, if I, for example, too quickly enable (or disable) multiple mods by quickly pressing the disable/enable buttons before Vortex has finished doing its purging, Vortex will fail to properly handle the game's .ini files, reverting them back to vanilla (or whatever version Vortex uses), forcing me to go back through and dig up every .ini setting one-by-one, from intro music of the vanilla game to enb and physics settings.
As already stated, this is happening on both my rigs--the HTPC and the gaming PC.
I've had some luck by creating a new profile and added a couple hundred bug-fix mods and others for testing. The purging issue didn't happen in that case, but switching back to the old profile brings back the purge issue.
I've already attached a set of log files, but there's been no fix.
It's weird that this topic is labeled as though it has a "solution."
This problem is destroying carefully curated mod lists that people have spent weeks putting together. It's been more than a couple weeks since this issue has been raised.
I've been a long-time user of Vortex and I generally prefer it because I really enjoy some of the "collections" available but, if this doesn't get fixed soon, I'll have to switch over to MO2 because Vortex is proving to be so broken that it's unusable.