There are only two major issues with CF cards:
1. if the CF card identifies itself as a removable device, then it might not be recognised on the Amiga or might be refused by HDToolbox and similar programs. Behaviour might be different depending on which driver you use, i.e. Kick 3.1 scsi.device, OS 3.9 scsi.device, IDEfix or something else.
If your Amiga accepts the card as a harddrive, then you are fine.
Some removable cards can be redefined as fixed with some PC software. AFAIK such software only exists for Sandisk cards, therefore if you cought a removable card of another brand, you've bad luck.
2. IDE devices like CF cards will produce corrupted data if the MaxTransfer value is too high. The maximum possible MaxTransfer value for IDE is 0x1fe00 (255 blocks of 512 bytes each). Unfortunately WB 3.1's HDToolbox defaults to 0xffffff which is way too high.
Make sure that your MaxTransfer is set correctly for all partitions, then you are fine.
If both of the above is taken care of, then the card should work, no matter which brand it is.