How to properly migrate from my external hard drive to a NAS setup?

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My current setup is kinda like yours, just with 4 external drives.. So i just bought a case and wil transfer parts from another PC to it, since it can hold up to 12 drives internal.

I use Debian 13, headless (not GUI) and my OS is on a SSD, while only some data is on same drive for now, but that will change, but my libraries is also on other dries that i have mounted in Debian on /mnt/ext1, ext2, ext3, ext4 and first folder then is data in each and then a JMS1, JMS2, JMS3, JMS4 and also a JMS1_2, JMS2_2, JMS3_2 and JMS4_2

JMSX is for read only folders for Jellyfin while JMSX_2 is read and write. So Jellyfin is not able to edit metadata on the libraries that is in production.

Is Jellyfin running in docker? If, then its very easy to maintaine, and i would recommend your to use a systemdrive for it (SSD) so jellyfin is faster and also prevent your HDD from crashing. (Theres a lot of plates inside it, so multiple drives is better then one big when in production) - personally i have 2 8 TB and 2 4 TB drives... The 2 4 TB was some i had lyting around, but i plan on using them for cold backup and also have a 18 TB drive with same purpose when i get the case.

I plan on using this case:
SilverStone Grandia GD08

For backup drives i plan on using OpenZFS (ZFS) and use that to use OpenZFS to copy data.. else i use "sudo rsync -au --progress /source/dri/ /destination/todir/ with screen so i can let it run in the background.