Commit empty during rebase 2.8.1 windows

So twice now during this particular rebase I have had this happen. All of the work in this commit after being applied is gone. The only caveat is that I had sourcetree running at the time, and I wonder if that is somehow causing the issue.

aaron@aaron MINGW64 /c/src/FORB (mybranch|REBASE 12/42)
$ git rebase --continue
Applying: Commit1
Applying: Commit2
Using index info to reconstruct a base tree...

my changed files were here

.git/rebase-apply/patch:59: trailing whitespace. Insert Into .git/rebase-apply/patch:60: trailing whitespace. core.Provider .git/rebase-apply/patch:61: trailing whitespace. (ProviderTypeId, Name, Description, AssemblyInfo, CreateDate) .git/rebase-apply/patch:66: trailing whitespace.

.git/rebase-apply/patch:72: trailing whitespace.

warning: squelched 41 whitespace errors warning: 46 lines add whitespace errors. Falling back to patching base and 3-way merge... error: The following untracked working tree files would be overwritten by merge: file1 file2 Please move or remove them before you can merge. Aborting error: Failed to merge in the changes. Patch failed at commit2 The copy of the patch that failed is found in: .git/rebase-apply/patch

When you have resolved this problem, run "git rebase --continue". If you prefer to skip this patch, run "git rebase --skip" instead. To check out the original branch and stop rebasing, run "git rebase --abort".

aaron@aaron MINGW64 /c/src/FORB (mybranch|REBASE 12/42) $ git status rebase in progress; onto 210fcac You are currently rebasing branch 'mybranch' on '210fcac'. (all conflicts fixed: run "git rebase --continue")

nothing to commit, working directory clean