Being waterboxed means no more desync issues! After realizing its not quite donee yet, I'm gonna wait until it is done and I might restart this project if it doesn't sync with the merged one.
After so many successful sync tests, I found one that desyncs!.. unfortunately I don't know how to consistently reproduce it. It desyncs on 3rd track which I suspecting it would. I had rewind enabled. I'm sure to fix it you just make a save state before the dropped input(or somewhere close to it) and just load and keep fighting with it until it syncs.