Depends what you use...
I think, for an ordinary recorder application, the effects are bypassed. In Capture application (Presonus), the effects are bypassed too, but with the added benefit that the settings of the Fat Channel are preserved and retrieved when opened in Studio One... Huge convenience.
I have no idea related to SD card recording, if there is any. But I assume that it works the same way as Capture does.
If you perform the recording on Studio One, Studio One allows you to specify to perform the recording before or after the Fat Channel, thus much more flexible... For example, you may apply gentle compression or a high end EQ boost to your recorded signal during the recording. Fabulous, ain't it?