I've faced a very similar issue the last few days.
Started happening Saturday around the time of the patch, i started getting a general slowdown of Atlas, from clicking 'Rejoin...' to the game finished loading up where i could move around was taking around 5-10mins instead of the usual 2-3mins, and once in the game my FPS was hitting an alltime low of 6-8fps in low settings instead of my usual 20-30 with my mid-range custom settings (never checked the exact number, feels around 20-30)
I validated files and it found one issue, a configuration file which it redownloaded, i tried the game again... same problem.
Occasionally it would time out, i would get either a general 'Lost connection...' or sometimes it kicked back with a BattlEye error... so i removed Battleye and redownloaded/reinstalled it... same problem
I uninstalled Atlas, redownloaded it all and tried again, was getting a bit desperate by this time... same problem.
Did some googling and found a blog post where they discussed FPS in Atlas and how to improve things, they had some switches to put in the startup options which i tried, and i dialed back a lot of the settings based off that guide... still same problem.
Given my install of Windows was quite old and my levels of desperation were growing, i thought id try a fresh install of windows, so i reinstalled windows, downloaded the latest GeForce drivers, reinstalled Atlas and tried again... STILL the same problem. A long time to load in, and once in game my FPS was below 10 regardless of High, Medium or Low settings.
So i installed a couple of other games to try to understand if the problem was my end or the games end... ended up running around in Fallout76 on High settings with a decent FPS (>30) - very pretty game at those settings - so im reasonably certain its not my machine.
Friend of mine directed me to this thread, so i tried the 'move movies to a backup folder' and that has resolved my long load time... its still feels a bit sluggish but im in game within a few mins of starting the application again, lost all the pretty background stuff but meh, im able to get in quickly. FPS is still in the toilet however
Checked Task Manager whilst the game was running, im hitting about 20% CPU, 60% RAM and GPU flutters between 0-50% - My PC doesnt feel like its under any pressure/stress.
I've run out of ideas now...
Spec; i5-4690 3.5Ghz, 16GB RAM, GTX 1070ti and everythings running off a Samsung SSD 850 EVO 500GB - 280gb free space remaining. Clean install of Windows, Steam, GFX Drivers and Atlas.
Anyone have any advice/Suggestions? Feels like its not my machine is the issue here. - Thanks!