The problem arises with series of more than 4 games with the same name such as Pokemon or Spyro. The first 4 games are appended 1, 2, 3 and 4 to their names while the rest are appended a hash from the ROM's CRC16. If you add games in the future and at some point backup, format, and restore, the first 4 alphabetical names are appended numbers while the rest are CRC16'd. The order in which they are chosen for the naming criteria will differ. This is why naming the SAV after the game to preserve linking only works with 4 or less games of the same type.
If you've ever had about 50 neatly named ROMs in the game and ever formatted, maybe to change the cluster size or for another reason, you're gonna run into problems. LFN lack of support is arguably SC's biggest issue, since a switch like this could crosslink ROMs and save files, causing their immediate loss upon running the games, which obviously won't recognize one another's saves and format them. The only true and definate solution to this is giving your ROMs names of 8 or less characters length.