When adding a flow and deactivating existing players for that new flow, Dorico will delete any manual staff spacing adjustments made to those players in other flows. This means that if you want to create a new flow and only use some players, you will have to redo your manual spacing adjustments from everything you’ve done earlier. As far as I can tell, this doesn’t affect horizontal spacing or item repositioning. It only applies to staff spacing.
It’s not a a bug per se. Staff spacing adjustments are a property of a page; they don’t flow with the music. When you make changes that impact the casting off, the relationship between a passage and the page it was in goes away, and so does the adjustment.
Since staff spacing is a page property, if flows are set to begin on the same page whenever possible at its worse this should only affect spacing on one page — the one which the new flow starts on. It sounds like what Nichyc is experiencing may be more comprehensive than that.
Tangential to staff spacing, I personally don’t see why adjusting staff spacing shouldn’t lock the frame, the same way note spacing locks the system. This would side-step issues.