Hi, Boyd. The fact that the wood has broken out from the boards with the groove side may be telling you that there is not enough wood left to refinish. Since the sanding part of the refinishing can remove up to 1/8", and if you figure that the floors were refinished every 30 years, you are already down to the 3/8" that was probably left after the grooves had been cut. Check to see how much wood is left before you decide on refinishing.
The caulk is a bad idea. It will not take any finish and may cause other problems, like fisheye, anywhere that it touches the wood. A better way to fix the round holes is to cut plugs out of a similar wood to that of the floor and glue or screw them in place, depending on the size. Gluing is OK if the whole plug is in one board but you probably want to screw them down to the plywood you added if the hole goes across more than one board.
Wood fillers are generally not suggested for floors since the wood will move with changes in humidity and the filler will not. However, in your particular case, filler may be the only way. The answer to the comments in the first paragraph will have a lot to do with what is possible for your floor.