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#at the branch you want to rebase into "master > mybranch"
git rebase -s recursive -X theirs master

#then a binary conflict will happen so now you must checkout the version of the binary you want

git co --theirs -- my-binary-file.bin
git co --ours -- my-binary-file.bin

#now you must stage the file
git add my-binary-file.bin

#finally
git rebase -Xtheirs --continue