Heres my problem:

I went out to the hot tub this weekend to remove and replace the filter. I killed the power to the tub at the tub breaker that it seperate from the tub.
After removing the filter, I went to turn the tub back on and it never did.

It appears no power is getting through the control unit. None of the jets, pumps, heater, light, anything are working when the breaker is turned on. When turning the breaker off, a faint click can be heard in the control box.

My initial guess is the gfci that is part of the control unit, but that is just a guess. the reason I guess that is that the test and reset buttons on the gfci are not functioning. The reset button does not press at all, and the test button doesn't click or cause anything to happen, with or without the power on at the breaker. Where do I go from here?

if you have access to a multitester, you should do some checks across both line wires before and after each breaker, to locate the probable cause

I finally had some time to do some looking... I did find 1 fuse which tests fine. I did pull the GFCI breaker in the control box out and it won't test or reset, so I'm still suspecting that.

My main question now is, can I bypass that gfci since the spa sub-panel out by the hot tub has a gfci on the breaker? Or is that just asking for trouble?

The GFI in the spa subpanel is so so at best. It only senses ground faults off one side of the circuit, and releases a contactor to break both lines. Several things can go wrong there resulting in an unprotected spa. The contactor can stick, negating the GFI all together, there is mechanical latency in the contactor so even when the GFI trips, there is still enough time to electrocute an occupant, if you get a ground fault on the non-sensed line, the GFI may not trip, etc...

Always best to use a GFI breaker that directly interrupts both lines at the same time, ahead of everything else.

WEll.. I don't think its the GFCI now. I went out last night and bypassed the onboard GFCI that I suspected was dead. (I put like colored wires on the same post) I fliped the breaker and nothing.. Though when flipping the breaker off, I do hear a noticable click from the control unit... a lot like a relay click.... any ideas from there (it was dark outside so I didn't look to deep, I will get back out tonight.)