Comment 1 for bug 1820109

This is a known limitation, quoting from https://forum.snapcraft.io/t/snap-layouts/7207

Layouts cannot replace an existing but incompatible filesystem object. This means, for example, that files cannot replace directories or symbolic links, files cannot replace a directory, and existing symbolic links cannot be redirected to a new target. You can, however, replace a directory with another directory.

Having said that, we may be able to lift this limitation. I will consider options and use this bug for tracking.