EPDM will keep the file read only flag during check in check out operations, if the local file is modified or its not with the expected read only flag (if its was checked in it should be read only and not writable) you will get this warning.
I've seen that error a lot with weldments
I got this message today when I was checking out a folder of files. I don't understand how any of them could have been writable when they were all checked in.
I have blamed it on a cashe issue. I am thinking that the vault hasn't updated the cash in time and this is when you run into the error. Windows sees both files and doesn't know what to do.
This is all speculation on my part if anyone has better answers let me know.
I have advised my users to be very careful with that error and make sure you agree with the error that it will wright over the file.