Are you saying you have taken the zipper out and are putting it back? If that is the case, you should be working from the end of the zipper up to the waistband. Idon't fully understand your problem, but I've sewn for over 60 yrs, and did alterations for the public for 15 plus yrs & all zippers are sewn from the bottom up. Are you altering the crotch area w/o removing the zipper? I am just too dense to understand your problem. Sorry. Would be most happy to offer advice if I knew what to advise.

I'm taking the zipper out from the bottom to about half way up just so I can take in the side seam a little around the hips. I guess I don't know how to get to sew near the foot of the zipper. the zipper foot can't get past the bump on the bottom. (where the teeth come together)

I watched a video on You Tube and saw that I have to use a different foot to the base of the zipper. I'm not sure which foot to use. I have a Featherweight machine.

I'm still confused...is the zipper in the side seam?

Yes, I think I understand now--you've adjusted the side seam and now you need to re-sew the zipper that you unstitched part way up. You say you are using a Featherweight and zipper foot. I don't think the machine will let you move the needle position, will it? Therefore, you should be able to move the Z foot to one side or other of the needle. Start by pressing your new seam to lie flat. If it is a 'lapped' app., stitch the under first, then stitch on the outside to the bottom and across. You don't have to go across exactly at the zippers 'bump', just below it. If your zipper is one of the invisible kind--they install completely different and you will have to remove and it will stitch from the top down. I believe I've done the best I can w/o seeing. I welcome criticism.LOL

In this sort of situation I often cheat and hand sew using a back stitch that looks like machine sewing :-)

Well. 'Whatever works' works for me!