OK, DH went down in the crawl space today, and found that the joists are 16" OC but span about 20 feet. No good for tile. Every other one is sistered, but, well, just every other one. The deflectolator doesn't have a calculation for that. So that probably explains the cracked tiles and also the scattered cracked grout. The space is too confined to get more 2x10s in there to sister the rest, so he's going to propose adding a beam underneath the floor at as close to the mid-point as he can maneuver around the pipes and ducting that's down there. He doesn't know if they'll bite on that (they're paying him for his time...he's a handyman, so they may not want to incur the cost of a few hundred bucks), but at least they'll be informed and can make a decision. In the meantime, he's going to just put some blocking between the joists underneath the two removed tiles. I know, not a long-term solution, but a temporary countermeasure because he's got to get the 2 tiles back in this week. So what should he do about the missing underlayment? Other advice?

Gluing will temporarily solve this issue but in doing so will cause more of the same issues in other parts of the floor. If you intend on replacing the floor in the near future then go ahead. But if this floor is intending to stick around for awhile then gluing is not a good idea. How much clearance did you leave yourself around walls when it was installed?

You probably can jack it up, but consider the cause of the sagging, it's probably moisture. The real solution is to redo the floor. If you do, consider using a fibre cement product that is truly water/rot proof vs the plywood that seems to be favoured in north america. Rot in such material exposed to moisture (of course the tile base should be made waterproof) is inevitable.

Maybe my comment didn't show up? Also, one of the problems with tile that's "lifted" is that dirt gets onto anything that's sticky (glue, adhesive) and that needs to come off first before using any seam sealer (which might work for you) In other words, seam sealer probably will only work on new. It might be worth a try, though. If I needed a very quick, very temporary fix, I would use caulk. You can get a similar color. Be sure to tape on each side of the gap (closely) then caulk (make sure to cut the nozzle hole small and then incrementally bigger until the caulk comes out the "right" size), then smooth it out while it's still wet (there are tools for this, but an old credit card type of thing works well). You'll need lots of paper towels because when you're new to this, more will come off than stays on. Do a tiny bit at a time, because the surface of caulk dries and becomes unworkable rather quickly. For the lifted bits, you'll need to use gorilla glue and weigh it down. Caution, don't get the glue on whatever you using to weight it....this stuff is very strong! Test it out on something first to get a handle on how it performs. Good luck!