We have some bugs in this area. To workaround the issue, Close the target project (from Project Explorer or Navigator 
view) and re-open again.

Glenn Schmottlach wrote:
> I am currently running the latest version of the IDE (Version: 4.5.1
> Build id: I20081125). I noticed that as I add more projects to my workspace the Target File System Navigator fails to 
show the files contained within folders on my target.
> 
> I'm not sure the number of projects that lead to this "tipping-point" but if I create a new (empty) Eclipse workspace,
 add my target, and then browse via the Target File System Navigator the files within folders magically reappear. It's 
really odd. The view consistently shows the directory structure on the target (no matter now many projects I have) but 
after a while the files "disappear". I'm not sure if the workspace is in some way getting corrupt or if there is some 
other error. All I know is that creating a new workspace seems to fix the problem until I create the 'nth' project . . .
 and then the files on my target (but not the directory structure) disappear. Can someone offer a fix or instruction on 
how I can trouble-shoot this problem?
> 
> _______________________________________________
> General
> http://community.qnx.com/sf/go/post30873
> 

I had no such problem until I'd updated the software Image on the MTP hardware. 
This indication really helped. Thanks!