I've turned my Poseidon X into more of a road bike and swapped a 46cm bar for a much more comfortable 40cm. The microshift groupset has an externally routed shifter cable that was purposefully long to accommodate a bar bag, but it's now almost hitting my left hand. If I were to cut the cable shorter and feed it back into the derailleur, would I need to index my gears or can I just adjust the tightness with my barrel adjuster and be on my way?
Excess cable length would be hanging past the derailleur pinch bolt. It sounds like you are talking about making the housing shorter. Specifically the housing closest to the shifter. Doing this will involve loosening the pinch bolt and pulling the cable all the way back to the shifter. Once the housing is chopped the process is going to be the same as installing a new shift cable. In fact using a new cable may be a good option. Once the cable is routed back to the derailleur and pinched, indexing the gears will be the last step.
I'd suggest indexing the gears again, especially if you have access to a bike stand. Some index shifting systems can be really picky regarding tolerances