We've fixed this problem in our 2.7 branch of wyBuild (coming in about 1 and a half months) to use relative paths instead of absolute paths. That is, you'll be able to move the project & the files without having to re-add your files.
In the meantime the only real solution is to either delete the files from within your wyBuild project then drag the new files in. Or use the wyBuild commandline to replace your existing versions with the changed versions.
Neither choice is ideal, I know.