This is a bit of a complex problem but I'll try to keep it short.
I merged a branch (lets call it X) into my working branch (lets call it Y). Now, unfortunately for me I have to go through each file from X and check if it's 'safe' to use - discarding chunks from certain files, keeping other lines, etc.
While working on Y -- through Sourcetree -- I have been staging files and committing (and pushing) once I know they are 'safe'. So I have a remote and local branch (Y) that is now almost completely good to go.
Then something bad happened and I removed the remaining 'yet to be cleaned / checked' files from my unstaged changes and restarted Sourcetree - I did this thinking that when I remerged X, it would detect that Y had already accepted most of X's files (or that I hade made changes -- making them more up to date than X) and display those remaining files that had yet to be staged from before. This did not happen.
I now have all the changes I have 'cleaned' / saved and committed, but remerging X does nothing - Sourcetree seems not to recognize that X and Y still have differences and that Y doesn't have newer / more up to date files than X (in some cases).
This is despite the fact that running git diff X..Y shows all the differences I need to track!!!!
Okay I managed to figure this out... mostly by accident haha.
So since my current 'remote' and working copy branch (Y) had all the changes I wanted, I reset branch Y to a state PRE merge with X, but as 'mixed' (keep working copy changes).
This allowed me to just re-commit the working copy changes to Y and then merge from X (had to do a force push to update the remote branch Y but this was no biggie). The remaining files (which I had yet to clean) now appeared again, letting me finish my days work.
If anyone else has this issue, this will hopefully solve it for you too.
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