If I remember correctly there was an issue a few years ago where the Seafile sync client flagged files that had characters not permitted in Windows. You might look here for an example.
One approach in dealing with this while the client was being worked on was to list the offending files and change (or omit) the offending characters similar to what I think you are doing with EasyFind.
For example, in a terminal go to a folder of interest on SeaDrive and enter:
find . -name '*[<>:"/\|?*]*'
You should see a list of offending files (hopefully not too many!) that you can then rename as needed.
This, of course does not address your need to search contents but does it serve as a workaround for file names?