Hi Joël, I think that the loss of memory has nothing to do with the new EPROM - it sounds like the buffer battery has given in. The Matrix-1000 was built long before EEPROMs became affordable, so the memory is kept by a buffer battery in the lower left corner of the PCB, a standard CR2032 battery that has been soldered in.
To everyone's surprise, these batteries still work - 20-odd years after the last M1000 has left the factory. I've just replaced the battery in my Matrix; after 25 years of service, it still produced 2.95 volts. Yet, at some point in time, the battery can no longer keep the RAM alive.
My guess is that the battery in your M1000 is very close to dying, and somehow in the process of exchanging all the chips, the RAM hold failed. Try writing a ROM preset to one of the RAM banks and see if it's kept while switched off - and solder in a new battery sometime soon.