Relative path support for Nix flakes

As far as I’m aware, Nix Flakes should have had support for relative paths for a while now?

For some reason, when I nix develop in my project on a new Nix installation or after I run gc, I get this:
error: cannot fetch input 'path:../js-dependencys?narHash=sha256-cayhXT6eRBgQuvfu1IKkJpqdjKkhdzRKYsUikx%2fQo%2fY=' because it uses a relative path

Strangely, this goes away once I do flake update. What could be the cause of this annoying behaviour?

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This comment in the issue probably explains it?

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You seem quite right, thanks for your pointer!

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