Depends how it is modded.
If it is all your own/free to use work that you replaced it with then OK.
Otherwise you are still distributing copyrighted music and samples so can't upload the SDAT and tell people to shove it in there. Chances are nobody would complain (the amount of stuff ripped straight from ROMs and uploaded to/link everywhere, and indeed those nice 2sf files all over the shop that have been up for years and years now both attesting to that one) but letter of the law and all that.
If the mod is a pointer/bank pointer swap to get it to play other songs, something to change the volume, or a in situ mod for looping (basically the sort of thing you could theoretically tell someone to open up a hex editor and overwrite maybe 20 locations with this) then it should be easy enough to make a patch.
You might still be able to use xdelta or something to turn the base SDAT (or even go for the whole ROM if you inject the new SDAT carefully into it, or otherwise make sure it does not mess too much else up in the ROM) into your modded one.