Maybe implement automatic or manual (with command) cleaning of outdated AA files (eg: older than 3 months)?
My server stores about 1.5k of data files, but huge part of them are useless.
//(FileInfo) file.getLastModified() ?

I'm not particularly inclined to delete old atlas data from within the game. 1.5k is a pretty small amount, in will go down now that the packet rework is live. If you want functionality like this, you could probably use a bash script like:

find ./world/data -mtime +90 -type f  -regex "aaMarkers_" -delete
find ./world/data -mtime +90 -type f -regex "aAtlas_" -delete

I haven't tested it, but you probably get the idea. The -mtime +90 is what tells it to filter out files that are at least 90 days old, I think.