I have a somewhat similar question. I upgraded to 6.2.2.91 last night, and immediately ran into an issue with the /rest not being able to find application.cfc (where a bunch of components were set). I tried all manner of fixes with applicationproxy but in the end, I took the quick way out, which was moving the rest component directly to the root, so application.cfc could be found.
Like Alex I also have switched to single mode in anticipation of multi mode going away. I’m happy with it, and for now it works perfectly fine, but now that I’ve set up a mapping to say /rest which points to specific component inside a specific site, what’s stopping that from being called on site2.com/rest ? For now that’s giving 404 on all sites on this server, so not a real issue, but I could imagine people having multiple sites with a rest setup on one server. Or other mappings in general, wouldn’t they then apply to all sites when set via server.cfm instead of inside a specific instance?
I actually didn’t plan this very well and paid the price. First mistake was trusting the latest update, which in this case was the mistaken 7.0.202 or so. So that crashed everything and I basically had to set up from scratch. Clearly the last time I’ll attempt an update like that without reading up first, hehehe.