CATIA V4 and V5 are similar in name only! If they had different names people wouldn't be surprised that the translation process is fraught with danger.
I have spent many hours investigating this subject, which culminated in the release of a product called "Passport to V5", (a customised version of "PrescientQA"). This tool analyses the CATIA V4 models and reports on the areas of concern, (e.g. reflect drafts do not exist in V5 yet).
Dassault's own tools can create confusion, as the copy/paste method may work with no problem, but the batch tool doesn't!!
My methodology is to run Dassault's batch migration analysis tool, (add "-batch ûe CATV4ToV5Migration" to the CNEXT.exe command). This will identify models with problems, but not what the problem is exactly. So analyse these problem models with "Passport". This will correct some problems and offer advise for putting others right.
There are other similar tools available using "Q-Checker" and "I/Check".
IBM's CIPO dept. have done a lot of work on this subject. See http://www-5.ibm.com/de/caeserv/cipo for white papers, etc.
For info on:
Passport to V5 (from TDCi) - www.tdci.eu.com
Q-Checker (from Transcat) - www.q-checker.com
I/Check (from Incat) - www.incat.com/index.cfm?app=cadcamcae&a=verifi