Hi Brian -
"Check File Contents" is used to verify that two files are identical at the time of the sync. It is not a chkdsk kind of option that you can use to verify the integrity of the files/filesystem. You can check it/uncheck it at any time in a folder pairs lifetime. When the feature is turned on, we create files hashes of the contents of the files and compare them against each other to see if they have unchanged ( normally we would just use timestamps to see if files have changed).
So you can check that option now and do a sync - it will take more time than usual and should tell you that files on both sides are identical ( assuming you have made no changes since).
Thanks
Deepa