Lavatory craft timers do not go down when you are not in the game. I don't think they go down when you are in a raid too.
My generator is on while crafting and I have lv 1 lavatory
I found 2 other reddit posts about the same bug:
From the SPTarkov community on Reddit
Explore this post and more from the SPTarkov community
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From the SPTarkov community on Reddit
Explore this post and more from the SPTarkov community
www.reddit.com