Yes, deleting the attribute along with content (or deleting the attribute along with modifying content) should "fix" this.

"Fix", as in a moment you think about potential concurrency issues... (Nexus might be serving up the exact file you are modifying/deleting).

Not really a problem for us, since if we're having to edit the file our inbox is already full to the brim with messages from angry developers

Thanks very much for the help, Tamás!

I realize this isn't how Nexus is normally used, but I doubt many Nexus users serve both ivy and maven descriptors to their teams either. Despite directly messing with the repository, Nexus is mostly stable.

One thing you should consider: same stands for Nexus as for Maven (in broadest sense): I believe what you have there should be a Nexus plugin (same is said for Maven, Mojo mojo mojo...)

You problem is perfect fit for "capabilities", similar to one that publishes Maven artifacts as OSGi bundles. Not really related, but you can read more about it here:
https://docs.sonatype.org/display/Nexus/Nexus+OSGi+Experimental+Features+-+Bundle+Maker

With "similar", I meant, that this plugin above does similar, as in it exposes OSGi bundles "on top" of a Maven2 repository... just like you do with Ivy on top of Maven2 repo...

Yes, ideally a more integrated solution would be better. Nexus should be controlling all the interactions with the repository. But as usual, it's hard to find the time...

After the reading the long set of comments, this looks like Nexus is performing as designed and that this is acceptable.