SourceTree merge conflicts showing as unmodified

I am currently rebasing a commit i made a month or 2 ago. On the merge it shows all the conflicts in the working copy but when i select a file to fix the conflict nothing shows up on the right. The file is listed as Unmodified. Yet i can see changes to the files in there respective history and they are listed as a conflict in the working copy. This dosnt happen for all files however, some show the changes and i can fix them fine. As a result of it not showing the changes my external merge tool wont open. I am using Beyond Compare and it worked great on other merges. I have also tried cherry picking form the original commit and it had the same results.

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Looked into it some more and when using command line it says that the files remote is deleted. I have also done rename-threshold=25 on the rebase with no better results.

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Also background on the commit im tring to rebase. I move a bunch of files to different directories and made code changes as well and both the directory changes and code changes are on the same commit

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