This file tells Git LFS to download all files when someone clones the Matomo repository. Thomas noticed that it is completly useless to include this file in the built Matomo zip and therefore I updated the build script to remove the file.
As your Matomo instance has been updated and the new update doesn’t include that file anymore, the integrity checker notices that it can be deleted.
Matomo doesn’t automatically delete files that are not needed anymore as that could end up in a mess, removing custom files.