Database files contains fragments are normal. It's like you're writing an article on a piece of paper.
After a few revisions, your paper wold consists of a few "segments."
DB reload is like copying the articles to a new piece of paper.
I usually recommend reload only when the DB has more than 100 fragments or the DB is very loaded, i.e., performance sensitive. Make sure you have enough disk space which contributes to disk fragmentation.
About missing primary keys, we are aware of these warnings. Thanks.
Leon Liu
DFM DB engineer