I was having trouble seeing the program options before tos2win would close, so I found them online. Will paste here for reference, there is a -A option for atari msdos for instance. This is the command I have used for my boot drive: dosfsck.ttp -A -v -r c:
dosfsck [options] device fsck.msdos [options] device
System administration command. Similar to fsck, but specifically intended for MS-DOS filesystems. When checking an MS-DOS filesystem, fsck calls this command. Normally dosfsck stores all changes in memory, then writes them when checks are complete.
Automatically repair the system; do not prompt the user.
Drop the named file from the file allocation table. Force checking, even if kernel has already marked the filesystem as valid. dosfsck will normally exit without checking if the system appears to be clean.
Save unused cluster chains to files.
List pathnames of files being processed.
Repair the system, prompting user for advice.
Mark unreadable clusters as bad.
Attempt to undelete the named file.
Write changes to disk immediately.
When queried, answer "yes."
Filesystem is an Atari version of MS-DOS.
Repeat test to verify all errors have been corrected.