Just to update you, I think I see the problem, yet do not have a "good" fix for it yet.
quota's are set on the file system by user and/or group. Not the directory.
Soo, I'd normally say, put the share outside the /home directory. However, since the quota is on the entire file system of the partition. You seem to have a couple of options.
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Have a user with no quota.
have a cron chmod the files in that directory to that user.
have your other users that access that directory have administrative privileges.
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Or better yet, maybe force the user in samba to be a user with no, or a high quota
then have the other users have administrative privileges.
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I am still researching to come up with the best option.
To recreate your issue, I created a share, then,
quota username
then changed the owner of a file in that share
then
quota username
and found the user now had less files in his quota
Remember, I don't know what I'm doing with quota. Just exploring the options..