Sergio,
That's really a good question, let me explain:
If you want to convert sims3pack file to package files, the CC in CAS and in game will remain the same.
However.....
You basically have to uninstall all your sims3pack files (the ones you're converting to package), to avoid conflicts.
What will happen with your Sims in game and in CAS, when you convert ?
The Sims will lose the CC they are 'wearing' and you have to re-link them to the same CC in CAS converted to package format. It works just like shortcuts to directories. The CC on a Sim, is all linked to CC in sims3pack-format to begin with. Now, if you uninstall the sims3pack-files and add the package-files, although the CC is the same, it will loose the link to your Simmies.
Again the CC will be the same and work the same, but you'll have to re-link the CC.
Some things won't work converted to package-files. For instance a house, both furnished or unfurnished, will not show up in game if you convert to package. You have to work with sim3pack-files for those.
Separate package-files or compressed (combined) package-files ??
There is
NO difference whether you use separate or compressed package files. So in this case, you won't lose the link to the CC if you compress package-files to combined files.
The only difference is, compressed files will normally be smaller in size, compared to separate files (not always though) AND it will speed up the loading of your game and speed up access to CC in CAS.
In addition, when a new EA update / EP / SP is available, you won't have to uninstall all your CC (when using package-files), as these are kind of 'separate' from the game as opposed to sims3pack-files (as the updates and spims3pack-files are both installed through the Sims3 launcher).
I hope this answers your question ;) If not, just let me know !