CFS stands for "stupid user didn't read the manual". HDToolbox always suggests CFS, because there is no way to retrieve the correct identifier from the load module. It's an input field, you should overtype it with the right value. Use PDS\3 a.k.a. 0x50445303 for PFS3ds.
What a mistake I'm discovering now! So, that's why I was always finding problems. I was using 0x50465303 for PFS3ds!!! Then I was using PFS3.
EDIT: Afortunately it doesn't delete the partitions, but do I have to use it in all the partitions or can I use for example PFS3 for DH0 and PFS3ds for the bigger ones?