Endnote X3 doesn't recognize/display filed citations

I recently used the trial version of EndNote X3 and liked it, and it had no problem reading the citations from my older version of EndNote.  I now have EndNote X3 licensed through my university installed, and now the 100’s of citations I had filed are now all “unfiled.”  At least the citations still appear to be intact - just completely disorganized among ~2000 citations.  I spent a long time filing all those references by category, and would appreciate any tips on how to recover their filing designations. 

Sorry, but I don’t understand what you mean by “filing all those references by category” - are you referring to using EndNote’s groups feature or some other method?  Also, are you running X3 using Windows and if so, did you upgrade to version X3.0.1.? When you installed the university licensed version of EndNote did you uninstall the trial version beforehand?

There’s a possibility that installing the university licensed version of EndNote may have overwritten the .Data folder that was first created by the trial version of EndNote.  So whatever work/changes you made while using the trial version is now gone due to the installation of the university licensed version.  If you kept a backup of your EndNote library (and the .xml file which oversees the reference types) and the .Data folder they would save you the trouble of having to recreate everything. 

I agree with CrazyGecko.  It sounds to me as if you may have lost your .DATA folder which must be retained in the same folder location as the library itself.  Did you move the .enl file without taking this into account?  Remember that if the .DATA folder is missing, Endnote will recreate it, but it will not have the original information in it, including groups and attached files. 

If you can locate the original .DATA folder, you can recreate a .enl file though.  in the folder where the .DATA lives, create a blank file called LibraryName.enl (same as the .DATA folders name).  Then open it.  It should magically appear and contain your groups, attached files, etc.