We have a server running an ext3 drive running Linux and then another workstation running Windows with a NTFS drive.
When users use Windows they use the NTFS and when they are in Linux they connect directly to the ext3.
We use rsync a lot to copy files from the ext3 to the NTFS and it works great, but when we delete files on the ext3 we also want them deleted on the NTFS and we use the --delete-after to do this. It works great but we would like it to query the user asking if they wanted to delete the file or not. Is such possible?
Also sometimes users use the ext3 then go into Windows and use the NTFS and make changes to it. Now if we were to sync the ext3 to the NTFS we would lose changes made on the ext3 before this. Is there a better way to make sure these drives are synced up better.
The reason we have it set up like this is mainly due to the lack of support for ext3 in Windows and my feeling that ext3 is a more developed FS than NTFS.
I think the solution here is to consolidate the two networked drives so you can eliminate this synchronization issue. You could run SAMBA on your Linux system to provide access to the ext3 file system to the Windows users. Alternatively, you could buy a network-attached storage (NAS) device - these tend to offer the ability to easily share with Linux, Mac, and Windows users. Personally, I recommend NAS devices produced by Synology.
Yes, it would be optimal to unify the drives (or just eliminate one). Rather than use Samba, you may want to experiment with one of the several ext2 readers for Windows (ext2ifs, ext2fsd, Virtual Volumes, etc.). (No, that's not a typo, you would mount it as ext2. Windows apparently doesn't support journaled filesystems. ext3 is, as far as I know, entirely backward-compatible.)