We solved this by running:
svn propget svn:externals -R http://repoURL
The output was used as a starting point for creating a svnmucc control file with the following content:
propset
svn:externals
^/external-source external-target
http://repoURL
propset
svn:externals
^/external-source2 external-target2
http://repoURL
And this was applied to the repo by running:
svnmucc -m 'Changing externals from operative to peg' -X controlfile.txt
The output of propget was quite different from the svnmucc format, so I had to do some manual work, and wrote a little PHP script to do most of the repetative work.
The only thing I was not able to do using svnmucc, was multiple externals on the same folder. Apparently, svnmucc cannot set multi-line properties on the same target. But we only had a few of those in our repo, so that was OK to fix manually using the TortoiceSVN repo browser.