Please don't try to reproduce this bug. You may lose important data!
Make sure [Configuration] CompareTool=%PATH% doesn't point to an invalid location before comparing files in the directory synchronization.
I encountered a very strange behavior in synchronize directories.
I synched to directories. Two files appeared as different (let's call them file1 and file2). They actually were different. I pressed Ctrl+F3 to compare the file1 files. A message appeared that a file couldn't be find. I switch to another TC window and saw that file1 disappeared - it has been deleted. I opened file2 on the right panel using Lister in the other TC window - no problem. Then I pressed compare again and now only a single file was different (file2). I looked into the directories using the other TC window and file 1 was gone on both sides. I compared file2 in the sync window and got the same error message. A switch to another TC window informed me that file 2 was deleted on both sides.

sync options:
[ ] async
[x] sub dirs
[x] content
[x] ignore dates
Both files on the same local disk (normal directories), full read and write access. I tested this on Windows Vista RC2.
Don't try to reproduce this bug!
Steps to reproduce:
1. Set [Configuration]CompareTool=C:\UnknownMergeTool.exe
2. Restart TC
3. Left side contains two text files named file1 and file2 in dir1.
4. Right side contains two text files having the same names in dir2. file2 in dir1 differs from file 2 in dir2.
5. store position
6. call sync dirs
7. Compare using the above listed options
8. Choose "Compare files" in the file 2 context menu.
9. Start another TC window. The files are gone!
I was able to restore all deleted files using Restoration.


Some thoughts: It seems TC thinks the files are temporary and then deletes the files - that's just a wild guess. I hope this is fixed very soon.