Have you tried setting this extention in VSS Explorer->Tools->Options->Custom Editor?
or
Could you try the following?
- Rename
ft000002 and ft000003 (whichever one you have listed under OpenWithProgids) keys under HKCR
and
HKML->Software->Classes
- Rename .sql record from
HKCU->Software->Microsoft->Windows->CurrentVersion->Explorer->FileExt
and from
HKCR
- Add just one association for .sql file using Windows explorer.
Check HKCU->Software->Microsoft->Windows->CurrentVersion->Explorer->FileExt-> OpenWithProgids You should not have ft0000xx files in there now.
Check if VSS is working as expected now if not revert the changes.