Just swap processors to change a plc2 to a plc5 will only work with some PLC2 processors. I've done a few plc2/30 conversions, it's a bit more complicated.
Another hardware issue to watch for: Some really old 1771 racks won't work with a plc5.
I also am not generally in favor of the conversion program. I've used it effectively, but it takes a lot of work to get usable output from it. Trade off is eliminating typos from reentering the program vs extra time to make the converter output useful. With a big enough program, I'll use the converter.
There are some areas that will not convert at all and may take a bit of detective work to convert. Messages are done in a very peculiar manner. If you see rungs at the very beginning of the program full of GET instructions that seem to make no sense, that's probably a messge.