This warning has the following cause and solution:
This warning message often is displayed when you have checked out the same file to more than one user or computer. It is displayed so you can be sure that any merge conflicts have been resolved. In some cases, this warning may be displayed even if no merge conflicts occurred, and that is potentially confusing. But, if this is the case, just click Yes and continue with your work.
If there were conflicts, and you did not open the source file to resolve them, click No and do so now. When finished, rerun your Check In operation.