Starting Dune 2.8 .merlin files are not promoted in the source tree any more.
In absence of .merlin files Merlin will ask Dune for its configuration using the dune ocaml-merlin command.

However, when upgrading from a previous version of Dune, some .merlin files may already be in the source-tree and these won't be removed without a call to dune clean. These left-over .merlin files will be used by Merlin but they won't be updated by Dune any more and thus Merlin will get out-of-sync if the project configuration change.

This can be confusing for users.

One way to answer that issue would be to raise a warning when such leftover promoted .merlin files are found in the subtree, asking users to perform a dune clean.

@rgrinberg does that feel like a reasonable solution to you ?

Also for maximum impact this patch would need to be released as soon as possible.