Trying to find out if Merging can cause CC to Disappear?

Hello!! =) So I have just recently organized and merged my CC for the first time, which was greatly needed as I have about 36g of CC. I was very careful to not merge any scripts and to try to keep all files as neat as possible. Now that I have merged I feel some CC may not be in my game, but I know it is also possible I may have misplaced some when I was moving .package and backing up content. In order to know what to do next I had hoped I could verify with someone if it is possible that I could have done something incorrectly when merging which could cause my game not to load some CC files, before I begin searching knowing I could have just missed the files in my back up. Thanks for any info in advance!! <3 Also I apologize if this has already been asked, I am still familiarizing myself with the forums, I do hope that I have asked in the right section. =)