git-annex filter-branch can be used to split a git-annex repository. However, the approach in splitting a repository then copies all objects into the new repository and drops unused objects. And dropunused updates location log in that situation, even when the location log didn't exist in that repository before. So, that approach leaks information about objects that were in the original repository into the split repository.

Splitting a git-annex repository is something that, when you need to do it, you may have good reasons to want to avoid any such leakage of information.

So perhaps add a feature that copies only the needed objects over to the split repository? Or update the tip with a better method that avoids this problem. --Joey