Scrivener Links disappear when comments/footnotes deleted

Steps to reproduce:
Select some text in an editor document.
Create a Scrivener link (to web or file, etc.)
Select the same text (or more) containing the link.
Create Comment or Footnote.
Delete Comment or Footnote.
Original Scrivener link is deleted.
There may be a reason for this behavior that I don’t see, but if there is, there should probably be an alert before the comment/footnote is deleted.

The link actually gets deleted when you overwrite it with the link to the comment or footnote–the text can only link to one thing at a time. I believe there’s a comment in the manual about this but I’d have to go find it. The same thing happens if you overwrite a link to a web or external file. This also happens in reverse–if you overwrite a linked comment/footnote anchor with a Scrivener link–although it’s less obvious because the text remains boxed and highlighted and the comment still will link to it, but it’s one-way–you can’t click the commented text to jump to the comment, only the other way around.

I see the conflict now with double linking – this is a limitation of rft, correct? Html can’t parse overlapping links either, now that I think about it. Otherwise, I could imagine a scenario in which a popup menu would allow you choose which link you wanted to use with simultaneously linked and commented text. Similarly, I suppose there is no way for Scrivener to “remember” the original link or comment, so that it would reappear when the over-written comment or link was deleted.

Yes, this is one of the limitations that is discussed in the manual. If you need to add additional notes to a single small area of text, it can sometimes be best to use inline notes instead, which are added to the text, rather than attaching to it. Another way would be to add the annotation before or after the text rather than on it. Text can only have so many anchors as there are characters, and character level notes can make the text awfully unwieldy to edit.

In answer to your last question, it won’t remember the prior link, no, but undo will step back before the destruction of the note and restore it.