Current concern security wise is that there would be "data leaks" that would result from the sync tool being used; for example, the sync tool producing indexes that when be stored unencrypted on disk.
You are correct to believe there is a risk of data leaking as a result of indexes. How much of a risk that is depends on what exactly is indexed.
A while ago, I lead a project to build something a little like dropbox. To compare directories across runs, we used the path name, a sha256 hash of the contents if not already computed, various timestamp information etc.
Clearly, if a sync tool were to store this information about files stored in an encrypted container, the attacker would also have access to them. The exact risk of that really depends on your given scenario.
I suspect, however, there are bigger risks in play than you think. Let's assume, for example, that on opening a file, your innocent piece of software creates a copy so as to not corrupt the individual - however, you've mounted the file system read-only, so it handily creates a copy of the file in your temp folder. Great, except - it just copied your data from an encrypted partition to an unencrypted one, thereby leaking it.
The same could be true of sync tools. This would be a fairly bad way to build one - but it is conceivable the tool could copy files to a temporary location in progress. Again, you have a leak problem.
To be a bit more realistic - let's assume the sync tool copies the files in memory by
mmaping them and copying between them. What if you experience a system crash during this update and your app happens to be core dumped? Heck, what happens if the truecrypt drivers' memory is core dumped too? It might well contain unencrypted file data.
The fact of the matter is you're unlikely to be able to deduce the contents of entire files from any of these scenarios - but like getting damp in your house, something will leak, somewhere. The only way to be totally sure you have everything wrapped up is to do the obvious: encrypt the whole lot. Swap, disk, everything.
So to answer the question you asked: an attacker can clean whatever the sync tool stores. Have a look. Grab Process Monitor, see where it is storing data and then look at what's in it. That'll tell you exactly what data is being leaked.
To answer the question you didn't ask: there's no way to be absolutely certain you are not going to leak something using a truecrypt container on an unencrypted system.