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Yes, if you're going to run TrueNAS (or another solution based on ZFS) you should really get rid of the PERC and get an LSI SAS card in IT mode so that the system can see the raw disks.
When you start your SATA swap, either use the onboard SATA ports (if there are enough) or get a SATA card (more ports, probably slightly better performance than sharing the onboard controller) and start the process I described before.
Thanks for you help, I will try this. I will wait until my first SAS dies on noraidSAS card and then get a sata pcie and one by one move to sas