When upgrading EQ software you should upgrade all CAS services on your solution. Also DCE and DRE are advisable to be running on the same version. And the upgrade can be gradual.
It is also advisable you do install all hotfixes available for 4.2.5.
Does the Equitrac Office 4.2.5 server software work with the 4.1.2 embedded software or do you have to update all copiers to the 4.2.x embedded software in order for them to communicate properly?