I assume the conversion tools were used to take the existing PLC5 program and morph it to a ControlLogix equivalent.
If so, you can create a map, which correlates old PLC5 addresses to the converted CLX tags. Under RSLogix5000 menu, click "Logic" - "Map PLC/SLC messages". This is where you define the old PLC5 address was, and what the new CLX tag is. This requres a PLC download.
For example:
PLC5 file N7:0 would map to N[7]_0 (sorry I don't remember the conversion syntax at the moment, so I don't know if N[7]_0 is correct tag in CLX) Do this for ALL tags that the Wonderware application references.
Wonderware should then see the tags as if it where a PLC5, I have not done this with wonderware, but I have with RSView32 projects and RSLinx without issue. I believe the exception was with string tags, that I had to convert to a CLX tag on the HMI application.