Using both watchdog timers in PIC
If I understand correctly you are asking:

"if i put my device in deep sleep mode will the WDT wake it up (or possibly reset it) because the micro controller is not clearing the register?"

The answer to this question is: who knows? PIC18 is a family and not a device, so I can't read the datasheet because I don't know what device you are referring to.

Anyway I am quite sure that when in deep sleep the main WDT would be disabled, or else I don't see why you should have another WDT to wake it up. Moreover, you can disable it for sure before going in deep sleep mode and re-enable it just after the device is woken up.

Please note that probably WDT and DSWDT share some hardware so it might even be impossible to have them working simultaneously.