There is a lot of information on this on the internet about Hybrid and non-Hybrid modes. My basic advice is to pick one method, and stick to it and don't bounce back and forth. If you're not sure which one to choose, then go with the default.
Bouncing back and forth between the two modes will create CATPart files that will be organized haphazardly and will be difficult for you and others to edit. But the good news is it won't corrupt your file, at least not too much.
The differences: the old "non-Hybrid mode" groups geometry into two places - Geometric Sets and PartBodies. The new "Hybrid mode" groups all geometry into a PartBody. There are pros and cons to both modes, but the biggest concern is using both modes on the same CATPart file.