I got over this issue by using git merge command with the --no-commit
option and then explicitly removed the staged file and ignore the changes to the file.
E.g.: say I want to ignore any changes to myfile.txt
I proceed as follows:
git merge --no-ff --no-commit <merge-branch>
git reset HEAD myfile.txt
git checkout -- myfile.txt
git commit -m "merged <merge-branch>"
You can put statements 2 & 3 in a for loop, if you have a list of files to skip.