Lose participation and map progress
There’s nothing to fix beyond what you already identified. Just say ‘No’.
Just bear in mind that when that message appears, it is triggered by whatever algorithm anet uses to optimise the number of active map instances. No one has made any sort of qualitative judgement that it would be a good idea for you to switch. You have to do that. If you already have high participation or you can see the meta is progressing well, just hit ‘later’. You then have at least an hour before the map closes.
I do think that personal participation should remain if you switch map via the “This map has low population” prompt. Switching a map shouldn’t invalidate the work you have put in towards the meta
If you’re in a meta never leave unless you have a party anchor to bring you back. If you do have a party anchor, leave, take the buff, and go right back to the original map it wants to shut and then let your friend do the same thing.