Not really a fix per-se, but a least a workaround:
--On the machine you compiled the -lg Project on, create a new Service Tool and create a Parameter Group 'All Params' (or whatever you want to call it) and add all parameters for the Controller you converted. I'm pretty sure you have to do it on the original machine that Compiled the new -lg Project or it will not work.
--Copy the newly created Service Tool over to a machine that is getting the 'Invalid Format' error via flash drive, email, etc.
--Power up the controller and connect the 'Invalid Format' machine to it via CG150, then launch the Service Tool you created.
--You should get the 'Invalid Format in File' error on the first system scan. If you do not, close out the Service Tool and try again. It took me a couple tries sometimes...
--When you get the 'Invalid Format in File' error on the first scan, immediately re-scan the system (File-->Scan System or press F4). You should be able to see Parameters and Checkpoints after rescanning. Strangely enough, once you do this, all Service Tools created for this controller (even ones created under the previous versions) will scan and see Parameters and Checkpoints normally.
It sometimes took several tries and I found that if you do anything besides re-scanning after the initial 'Invalid Format' scan, it doesn't work. The main drawback is that you have to do this on any machine that exhibits this error... in my case, I had several Field Service guys and customers that had to do it, so I suspect it has something to do with the machine that I compiled the -lg conversion on... the fact that a Service Tool created on that same machine seems to be the key to fixing it seems to support that hypothesis. Unfortunately, Randy was unable to reproduce so it remains a bit of a mystery why this happens. Perhaps as more people run into this they will be able to gather enough data to pin it down.
Hope that helps... if you cannot get this to work or doing this on all your Service Tool machines in the field is not an option, you'll want to start from scratch with a new Project built around -nl hardware... that's what I ended up doing before I was able to figure out this workaround via trial and error. I got pretty good at exporting and importing pages, and it ended up being a good opportunity to clean up my code. Having two machines with a full version of GUIDE side-by-side makes it a fairly painless process, just a little time consuming to make sure you hook everything back up correctly and you have to pay close attention to signal naming to avoid mismatches between pages.
Good luck!