The Houston GM has "sort of" lost all his minor league players in the online league Extra Innings.
Link to .dat files:
www.bemont.net/Bug.lg.zip
On the ML transaction screen, he has zero players at each level. In the minor league batting and pitching rosters, he has zero players. However, you can access many of these players by clicking their names in the depth charts, lineups, and pitching rotation. You can also access them on the html transactions list, in the minor league system report and in the player development screen. In each case, the player is still supposedly on that minor league team, and, in fact, individual players can be returned to visible status by moving them to a different minor league team.
However, I have tested with a copied file, and they will not play until they are returned to visible status.
The Houston GM tells me that prior to this sim he delegated to minor league managers minor league transactions.
Edit: I see you wanted the file sent to you by ftp, so it is on the way. I named it Extra Innings. Same file you can download from my link above, even though there I called it Bug.