I was able to get things to regenerate via a combination of sleeping for 24 hours and then idling in game for a few minutes.
That being said, there are other reasons why your purified water may not be showing up. I've had an issue where, for weeks, Sanctuary wasn't storing extra water even though it should have been. There appears to be a bug (or undocumented feature) related to inventory in the Aid section of a settlement's workshop. Removing dirty water and purified water from your workshop appears to allow another batch of purified water to spawn.
I have been experience this issue for weeks now in Sanctuary. When I took over The Castle, I temporarily had purified water being sent to my workshop, but it stopped after a while as well. Both settlements produce over 100 water and have sufficient food, defenses, power, and settlers to keep things running. The machines are powered and active.
After reading through a fair amount of misinformation (you don't need empty bottles in your workshop) and bad assumptions on the Steam forums (see links below), I came across one theory that held some merit: People claimed moving some aid items from their workshop was addressing the issue. Some claimed you just had to move dirty water and purified water, others claimed you had to remove everything.
To be safe, I built an ice cooler in The Castle and moved everything from the Aid section of both workshops to it. Then, I slept for 24 hours. Both workshops were still empty. I left my console running for a few minutes while I went to do something else. When I came back, the water (and crops!) I was over-producing were finally appearing in the workshops of both settlements.
Initially, I removed everything in the Aid section of my workshop just to be safe, and purified water started spawning again. I've since re-added everything but dirty water, purified water, rare chems, and cooked food to the workshop and I am still getting purified water. I think the issue is related specifically to having water already in your workshop, but I have not verified that rare chems or cooked food might also have an impact.
It doesn't appear to be related to anything your settlement overproduces. The Castle generates more crops than I use, but not clearing out the excess crops hasn't prevented the purified water from spawning.