Poking rescan is not the only thing rescan-scsi-bus.sh --forcerescan
does. In force mode it will attempt to sync in flight writes, and remove and re-add devices. Poking the delete files of a device, similar to what you might do when removing a LUN from a live system. Per the warning in the usage message, this may be dangerous, try without it first.
No, this is not a configuration flag, as such. It is a way to tell the kernel to do something. On a restart, the kernel needs to scan the storage system anyway, so persisting it has no purpose.
I am not aware of any disable value for the sysfs knobs. Although this API is dreadfully obscure, I may be missing something. If your LUNs are not in a good state after a minute or two after issuing a rescan, doing it live may not be feasible. Stop applications using the disks, and reboot as cleanly as possible. By the time disks are not working, may be a bit late to do a backup of data, but do any recovery you need to.