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Yes, with the current code on the desktop (and due on the iphone in 1.0.2), multiple client files can exist for a single client. This is in order to help us avoid thinking that the database has been reset when in actuality the issue is that another client is in the middle of updating the sync database.

These extra client files are removed in subsequent syncs (from the same client) if they are too old (I think they get removed if they are over an hour old, but that timeframe is subject to change).

As an aside, if your files are getting really large, there are a couple of things I can think of offhand to check. First, make sure that you don't have clients that are too far behind on syncing. We have to leave transaction info around for the least-recent client, so that it has all the information it needs to merge changes. If this is the issue, getting all of your clients in sync will result in all the old transaction files getting cleaned up. (Unless there is data corruption, in which case your best solution is probably to get a known-good desktop client, do a database backup via File -> Back Up Database, then restore from that database via File -> Revert to Database Backup, then sync and push your local database to the server, then have any other clients sync and reset to use the server data.)

Second, be aware of what kind of data you are putting into your database. If you are making voice notes, for instance, those are going to take up a good bit of space, especially if you are still using 1.0 on the phone as we weren't compressing the data as intended at that point. Also, while when you drag in files we default to making a link, you can defeat that by option-dragging, which will embed the file, likely bloating your database. One customer also reported that they were dragging in files which were getting embedded, but it turned out that they were dragging the files in from another application which wasn't providing us the (normal filesystem) link information, they were providing the entire file on the pasteboard, so it was all getting embedded.