As you state others have no issues, it would seem to be related to the setup on those writers' machines.
I think I'd approach it like this. Since you are referencing source control, this would mean the real content exists in the source control server. So you should be safe in totally clearing out the Working Folders of the affected PCs. So start there. Delete all files from the working folders of one of the affected PCs. Then open one of the projects that was issuing the warnings (your image listed simple warnings, not errors). This action should cause only the needed files to be copied down from the server.
Then compile and my guess is that the issue will have resolved itself.
And last but not least, I'd also ensure I had a decent backup of the folders in question before I did anything.
Thank you, Rick. We have tried deleteing all .CHM files from the local computer of the user who is having the issue. We have even deleted all .CHM files from her recycle bin, but that has not worked, either. We have deleted the .CPD file and reopened the project, and the warnings are still appearing.
Note that in one of the projects with this issue, the compile completes, and everything seems fine with the compiled file. In another project, however, the compile never completes, so this is a bigger concern. The warnings in that project are similar to those shown above.