I went to super search to look for non-replies that had "personal" and "nodelet" in their titles and quickly found what I was looking for: Personal Nodelet Extractor and Personal Nodelet Restorer.
I didn't look at them to verify my recollection, but I believe you can use them to backup your personal nodelet, edit it, then upload it again. I also recall these not handling some types of links, but it sounds like you are mostly using lots of node-ID-based links, which would be what they'd support first.
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