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Further digging lead me to discover that its nextcloud that cannot handle the 7000 folders or more and not the centos server. I am able to sync using sftp protocol and found an amazing app called FreeFileSync.
It can create a mirror image which is awesome, because I want A to be copied to B, but also I want it to remove old files or versions on B, and I do not want it to delete on A if I delete on B. Something that goodsync and other utilities cannot do.
Basically, it works just like nextcloud, but its not as resource intensive and it can handle more files. Nextcloud is nice, but for now it has to go back on the shelve until it resolves all the current bugs.
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