hives.cfg
https://gist.github.com/TomeWyrm/66d793e85d4317d94d92

bees.cfg
https://gist.github.com/TomeWyrm/b0f64c8a06c281d16833

I broke the custom hives and only got Valiant bees. I have no idea what I did wrong... help?

Your species names in hive definitions are wrong.
rocky should start with a capital letter and I'm not sure where embittered and water came from, it's not anywhere in bees.cfg

If you check your log you should see something like:

[21:08:38] [Client thread/WARN]: gendustry.bee.rocky is not a valid bee species in hive definition Rock
[21:08:38] [Client thread/WARN]: gendustry.bee.water is not a valid bee species in hive definition Water
[21:08:38] [Client thread/WARN]: gendustry.bee.embittered is not a valid bee species in hive definition Nether

See here for the right names: https://gist.github.com/bdew/f0b7a216eea8e32d9095/revisions

Also watch out for capitalization - it's case sensitive.