Loadouts were obviously much needed and appreciated, but how the game remembers your inventory at the end of a session should work like it did before. Currently all it remembers is the last loadout you selected, and disregards anything you might have added to your inventory since then.
The way I use loadouts is that I have one for each map I own (sidenote: I'd really appreciate it if there were at least as many loadout slots as there are maps). But sometimes I'll bring a certain piece of equipment that I don't want to be a permanent part of that loadout but is useful in the short term (for a particular mission or a weapon type I'm grinding or something). If that short term need extends between sessions, though, it's frustrating because the game will remove those non-loadout items from your inventory when you quit the game.
Most things in the game (besides your location) stay just as they are between sessions, so it'd make sense to me for the inventory to be that way too, like it was before loadouts were added. I think some of the complaints we've seen about the loadout system may have this change as their root cause. Maybe a message either at quitting or starting a session that says "Some items in your inventory have not been saved to your current loadout" would be helpful too, though I'd like a "Don't show this again" checkbox if you added it.