doHOOPS identifies players by their name (and a hidden ID number) -- not by their jersey numbers. If a player needs to wear a different jersey during a particular game, just change the jersey number shown for him or her in that game's lineup. (Always change the jersey number for a player, not the player for a jersey number!)
If some of your players wear different numbers depending on whether they're wearing their home or away jerseys, doHOOPS handles that, too. Just tell doHOOPS which jersey number you want to use on your reports, the home or away (dark or light) jersey number, and that's what you'll see for that player in most doHOOPS reports.
More details about jerseys numbers are available in the Players window.
Tip category: Recording games
» Recording games
Tracking fouls during a game
If you get to the game late
Lineups vs. rosters
» Jersey numbers
Using the Override Scoreboard
Shot Locations, Layups, and Points in the Paint