How old is this installation? All modern Isolation installations use brown, orange, and yellow. This would mean that all the circuits would have to be rewired .
What is the primary voltage to the transformers? This could mean alot of work if new feeders have to be routed to your new panels. In any case, in the very least you would have to pull a second ungrounded conductor or a neutral, (what ever the case may be) even if the existing conduit could be used.
If these are going to serve patient care areas, you will have to retest the grounding system in these rooms.
These are just some of the things I see might be problems.
In reality, if these Iso systems are not needed or required by any local or state amendment, I can see doing away with them. For these to be in service you have to do the yearly testing and problem solving periodically or as you said repairing.
[This message has been edited by Roger (edited 04-04-2003).]