Updating Device Certificate and print drivers on network printers causing problems for end-users

I'd like to get a better understanding of the effects of changes to established network printers for end-users.

Problem: Users for some of the printers have to go to the machine and manually choose to print the document each time. It seems to be a mis-match from their print preferences and the settings on the printer.

"Fix" I did to get them back in business: Changed settings on printer for paper weight from letter size to auto-detect, and to use machine settings instead of driver settings. Also had them uninstall the printer on their computers and reinstall it. (All had the print object in Printers & Scanners associating their printer host name to a decommissioned print server - done several months ago.)

Background: I work for an MSP that provides leased printers and full printer tech support to an enterprise healthcare organization. I'm still new, been here about 6 months. I found that over half the printers were using device-specific drivers rather than a universal driver (PCL6 - a V3 driver), and that the Device Certificate had been created at the configuration center before it was shipped and used the random name that is self-generated (i.e., RNP......). The printers aren't in the client's Active Directory; they just reside on the print server. I thought it prudent to update all the print objects on the print server so that all used the same PCL6 universal print driver (makes it much easier when we do lifecycle replacements), and to create new Device Certificates using the assigned Host Name. Rather than being seamless or "invisible" to the end-users, it's causing problems and I don't understand why.

Would someone explain what I did wrong (and why), and how I should have done it.