I give a reply to the last comment of Arjan here to give some screenshots.
What I did is this: Downloaded from the team server the application to a new directory. Updated the userlib directory with a new .jar file. In this example with a new jasperreports-4.1.2.jar. Made some changes to the application and did a commit to the team server. As you can see from the picture the .jar file is not synchronised.
Here again an answer because of the limited comment possibilities. You triggered me to look in the history section and this is what I noticed:
The jar file was there already there when I committed revision 39. I know this for sure because of the comment I made to this revision. But the file only started to appear in revision 41.
I have checked the teamserver again by downloading it to a new directory and the file is there. Strange though that the original directory still gives me the above picture that the .jar file is not synchronized. I do not know what is causing the delay.
If you replace a library with a newer version and the commit using the Modeler, the library should appear in the "Changes on disk" tab page of the commit dialog. Does it appear there if you try it again? If it does not, it is a bug but I cannot imagine that there is a bug in that functionality.
If you commit outside the Modeler meta-information is missing and the Modeler cannot determine with which version was used to commit. To get around that you can do a bogus commit (change the canvas width of an arbitrary form) and the next revision will have the correct meta-information again.