I am a newbie git annex and english is not my native language. Please bare with me. After evaluation so many options, I have decided to keep track of my family photo collection via git annex. My family photo collection is around 300gb and consisting of 120K items currently and its getting bigger fast.

Previously, I was using my home server and attached usb disks. I had also cold backup disks. But keeping them in sync without making errors had been troublesome.

For this task, I decided to use three external usb disks along with a directory in my home server each keeping a git annex repository. I use my desktop as source annex repository to upload photos to these git annex repositories. I will keep external disks off site and rotate them off and on.

I have implemented this design but I have run into a problem.

Currently, there are five git annex repositories as described above. One of them is on the home serve internal disk, three of them are in the usb disks. One is in my desktop harddrive. Apart from my desktop repository, all other repositories are configured as "standard/backup". My desktop annex repository is configured as standard/manual. Each repository has four remotes of other repositories. They can all sync each other and get the contents. However currently I am receiving git message from all my backup repositories as follows.

Auto packing the repository in background for optimum performance.
See "git help gc" for manual housekeeping.
warning: The last gc run reported the following. Please correct the root cause
and remove .git/gc.log
Automatic cleanup will not be performed until the file is removed.

warning: There are too many unreachable loose objects; run 'git prune' to remove them.

I have tried git prune --dry-run as suggested some internet sites and I have seen that git wants to remove almost all annex blob files.

The annex repositories are mostly on btrfs file system, one is on ext4 file system, I do know if it matters. Git-annex versions are 10.20230126-9 in every machine (arch and manjaro).

git annex unused gives nothing. I am not using any encryption or any other git pluggable system other than git-annex.

Could you provide some insight please. Is there something wrong my repositories. It really took days to upload and sync all these repositories. Any help is much appreciated.