If the locos were programmed correctly with a different DCC system they “should” work with all of our equipment with no changes needed if that old system follows the NMRA standards of programming.
A few things to remember: 3,03,003,0003 are DIFFERENT DCC addresses!!! A loco can have a short address (two digit) OR a long address (four digit) but only one of those is active at any given time.
3 and 03 are short addresses . never enter leading zeros of a short address
003 and 0003 are LONG addresses.
The other possibility is issues with consisting / MU lashups / multiple loco sets. If you consisted or created sets of locos to run together with your old system they will not work with your new system.
To resolve this you must reset the locos to factory settings then recreate the consist on your new system.
Programming on the main will only work if you know the existing locomotive number AND the loco will respond to that number when given a command. Typically I check this by trying to flash the headlight multiple times or trying any button or function or speed command. If it will respond to something, anything at all, then you can use POM. If you get no response from any command at all under normal operation usually POM will not work due to the fact that the loco address is wrong.
If you want to add a dedicated programming track to the Power Cab you can use the Auto SW. basically it is relay board that gives you the ability to switch between a dedicated programming track and a main track.