Paint is bubbling-how do I fix?

I recently painted my dining room with Sherwin Williams duration paint in a satin finish. afterward, a shelf fell down and left a large hole in the wall. we decided we didn’t like how overly shiny the walls were and how it showed several imperfections where we tried to spackle other smaller holes. we had a drywaller mud the larger hole and other imperfections. we sanded the entire room, primed The Whole room again with Sherwin Williams, and we painted with Sherwin Williams eggshell but mistakenly got pro mar instead of duration. the color looked wrong and when we talked to Sherwin Williams they said the colors won’t match exactly between duration and pro mar, plus the change in sheen makes it look different.

we were unhappy with the color. so we got behr paint color matched to the duration paint. it actually looks very close! we painted The Whole room again (without priming). that evening, several large and small bubbles popped up. We scraped the loose edges and then We put drywall mud over them and plan on sanding them down in three days to give it plenty of time to dry.

1. I assume we need to put primer on those spots. Should I use something like Kilz? Is that oil based and will that be a problem if my paint is latex? Or is another regular primer acceptable?

2. i will repaint using the behr paint Just over the newly repaired areas.

3. do I then need to put a coat of paint on the entire wall again so it all matches? It is a dark navy blue color.

4. have we done what we needed to do to prevent the bubbles from appearing again?

as an fyi, this is not a wall adjacent to the exterior and no bubbles popped up after we put the original primer and Sherwin Williams duration on the walls. I don’t know if the bubbles was due to the mismatch in sheen that we may have failed to completely sand off, possible drywall mud that we did not let dry entirely before we repainted, or something else!

Thanks!