Recovering from forgetting to .gitignore

I forgot to .gitignore a particular file, and adding it to .gitignore after having committed makes no difference.

Well, of course it doesn't. Ignoring is about untracked files (which means files not under version control).

I found a page on gitready which explains how to remove a file from the repository without removing it from the working tree (by using the command git rm --cached <file>, which works ok, except that if I then try to merge that back into another branch, the files in the working tree get deleted.

Git deletes file because you can recover it, as it was tracked in one branch.

The solution would be to commit "untracking" a file (removing file from version control) in all branches, using git cherry-pick, or making git rm --cached <file> && git commit -a on a separate commit branch, then merging this topic branch in all branches (and then recovering file from a tracked version).

Rename the file to a temporary name (not using git), commit the deletion plus the .gitignore file, then rename the file back to its original name.

mv wantnot.txt wantnot.txt.tmp
git rm wantnot.txt
echo wantnot.txt >.gitignore
git add .gitignore
git commit -m "remove mistakenly committed wantnot.txt"
mv wantnot.txt.tmp wantnot.txt

Your use of a separate branch for this may be unnecessarily confusing the issue.