You have to basically uninstall
all your sims3pack-files first, before converting them to package-files (or re-downloading these files and than converting them). You can't have both sims3pack-files and package-files of the same CC, cause this might conflict in game.
However if you uninstall the sims3pack-files and "replace" them by package-files, you have to re-link the content to all your creations using these files (Sims clothing to Sims & furniture to houses for example), as sims3pack-files are a bit different from package-files and in the conversion the creations lose the links.
Please note, the only thing you can't convert to packages-files are the lots itself !!
I hope this makes some sense.
Groetjes, Cheers, Gruessen,