I'm assuming this is a bug, but water purifiers in your settlement will not generate and store excess purified water in your workshop if you have any stored there already.
I wanted to mention it because I've seen a TON of guides recommending that people build water purifiers to sell off excess water and even MORE forum topics/Reddit posts asking "why do I still have only 5 purified water in my workshop storage?", but maybe only 2 cases where someone brought this bug up.
I had 9 water purifiers running (with maybe 13 settlers) and the stock of 12 purified waters in my workshop's storage didn't change in about 7 hours of playing. I took those 12 waters out of storage, and maybe 20 minutes later I found 40+ units of purified water in my workshop.
I built a little trunk/chest (in the furniture section of the build menu) to keep my water from now on, to get around this. Hopefully stuff stored in player built storage is safe from raiders/settlers/game engine cleanup processes. I don't know for sure, though.
*edit: This MIGHT not be the case if you have supply lines running between settlements. The fact that I have seen so few mentions of this weird workshop caveat leads me to suspect that there might be some other factor (such as supply lines) that also deals with this bug*
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