Yep, still happens for me. There was a release (maybe 5 or 6 versions ago?) which said it was fixed but it's never been sorted. Every time I open a project after a Wappler update it goes back to the default bootstrap theme. I only have to click the rocket icon to sort it, and that's become a routine now, but if my target is dev then it uploads the plain theme and I have to them re-upload the custom one.
Git shows the changed file until I click the rocket icon which then causes Git to no longer show it as it's back to how it was before.
Yes.
I recall @George saying that it does a date/time check and sees the new Wappler files as newer so uses those instead but if we're using custom themes then this check needs to be ignored.