Hello out there!
I am retiling and am down to my subfloor. The existing toilet flange is not mounted to anything but the three inch sewer pipe. A square hole was cut into the subfloor and the flange was brilliantly lined up so that there is nowhere for the screws to go in. Someone dropped some long nails into the four holes but they grab nothing. The flange is also crooked by about a 1/4 inch variance. There is a wee bit of play in the flange and pipe. I am hoping to not have to cut out and replace the subflooring! Could I use the extra slots that the closet flange bolts would fit in? The long square slots in the front and back of the flange which are not being used to bolt the toilet down ? What about the fact that the flange is not level? Any fixes out there?
Many thanks!

"NOt level" is usually not a problem as long as it is not also above the floor. If those openings can be used to fasten it, then use them.

can you cut a slot that will be hidden under the toilet base and slip in some blocking to screw into? the blocking will act like a sub-sub floor.
as for the tilted flange, secure the higher side first and snug the lower side but not killer tight.
make sure to use solid brass bolts and nuts, not plated steel to set the toilet.

if you are up for it redo the sub floor. Secure the new flange to the floor with good fat brass wood screws. Underneath use a no hub coupling to connect to existing drain. From your post I think you will sleep better.

You would be better off in the long run to replace about a 16"x24" rectangle of sub flooring. start at the flange and cut away from it till you hit the joists, then mark 3/4" to the center of the studs. Find both joists this way mark where the joists are. 2" from the back of the flange mark the top of the rectangle and go 24" from that mark to mark the bottom. The joists will be the sides(plus 3/4" on each side). once you remove the subfloor, you can cut off the drain line about 5-6" down and install a coupling and new pipe that extends 4" above the new tiled surface of the floor. Mark and cut a new piece of subfloor and secure it to the studs. Put down your tile backer as normal, and tile the floor, and leave 1/2" all around the pipe open. After tile is down, cut the pipe off flush with the floor, and put the flange on it to align the mounting holes and mark them with a sharpie on the tile. Remove the flange and cut slots with a grinder for screws to go through, or use a diamond grit hole saw to make openings for the mounting screws. At this point, I put a bead of silicone down on the tile under the flange, and get it around the screw holes in particular, glue the flange, and slide it into place, lining up the holes. After the glue has set for 45 seconds, I run the screws into the flange and secure it to the subfloor and put a dot of silicone on the screwheads and smooth them over, sealing them in. WIth a sawzall and a drill, you can complete the repairs up to and including the tile backer in 20 minutes or so if you are proficient, slightly longer if you aren't comfortable with them.

I would put the flange on first (loose fit) and cut the pipe flush with it.

The big "IF"

"IF" you have a crawl space under the toilet. Following will avoid needing tile floor repair.

1. Remove the existing flange and first piece of connecting pipe. Clean away any loose material. It will depend on condition of material under flange and above sub floor if all should be chipped away/removed.

2. Cut a piece of 3/4" pressure treated plywood wide enough to just fit up and BETWEEN the floor joist with other length of about three feet or so.

3. Either take very good measurements OR just hold cut plywood up in place under existing toilet hole and have someone above in the bath mark the exposed new plywood to determine where to cut hole for the pipe. Drop the plywood down and cut round hole for size of pipe penetration.

4. Attach plywood up and under toilet with lots of proper screws, not nails. (Best to have someone above verify new hole is in proper position during attachment.) Recommend using spray bottle to treat sub floor and pressure treated plywood with some type of water seal.

5. IF original opening is completely clean of debris/tile cement etc, lay new toilet flange over opening, properly align and mark/drill at least four (or six) 1/4" holes for toilet flange attachment bolts.

6. Pre-Fit new connecting PVC pipe and toilet flange to proper height above existing tile floor. (Face of flange should be at or slightly less than 3/8" above tile --- not more. Use PVC flange with stainless steel insert.) This will determine amount of "spacer's: needed -- if used as follows.

7. IF opening is completely cleaned out and flat, fill space UNDER new flange with several 1/4" and/or 1/2" PVC extension rings used as spacers, BETWEEN original sub floor and BOTTOM of new toilet flange. OR fill space with proper tile cement. If spacers are used apply !00% silicone during installation as noted in (9) below.

8. After flange and pipe have been installed in place, use 1/4" STAINLESS steel bolts, fender washers and nuts --- ALL stainless steel. Bolts will need to be aprox 3 1/4" to 4" in length. If fully threaded bolts not available, ensure length used has full thread showing thru new plywood in crawl space. Bolts should extend down thru existing sub floor - thru new plywood and into crawl space. This will secure toilet flange regardless of condition of original sub floor.

9. Fill opening around pipe/spacers with 100% silicone caulk. Not caulk "with" silicone. Or tile cement. Fill completely so that any possible future leaks of toilet wax seal will not be allowed to penetrate down to sub floor and cause damage. If PVC spacers were used, apply silicone between spacers and any holes to seal water tight.

Not a plumber. I understand a professional would probably never use the above procedure, but IMO it is a reasonable approach for a DITYS'er to accomplish a good repair, especially when the sub floor has water damage.

IT would be a VERY complicated procedure, and much more work than necessary.