I had the same problem, except I'm running nextcloud-aio so I'm not able to mount additional folders inside the ncdata folder.
After trying many things, the solution that seems to work is preventing the mover from moving this file to the disks from the cache. I'm using the Mover Tuning plugin to achieve this.
Steps:
Stop all NextCloud containers
Delete the rootcert.crt file (make a backup, just in case)
Start nextcloud containers again. This will recreate the rootcert.crt file on the cache (SSD).
Install and configure the Mover Tuning plugin to ignore this file when moving and leave it permanently on the cache. I used this guide to do this.
Hope this helps.