Also be carefull if you have included files that have includes that aren't in the project list.
I know, I know, it's bad practice, but when I was dealing with the number of files limit, I would debug and have one of the 'modules' for a flash page all set, then basically take it out of the project other than the reference to the 'main' file for that flash page. As I did more and more pages, only the 'main' file for each flash page was referenced. Idealy each of these modules would be 'locked down' and the source archived and not changed unless absolutely necessary.
When I made up a 'reference tree' for my files and functions, I not only had to scan all the main files, but any included files, and then those included files, to make sure I caught everything.
With a CW license that allows me to have sub-files, that problem went away, but I still have to be carefull if I have to deal with older projects and code.