Once you have them DRM-free, in whatever format and by whatever means, then yes, calibre will convert them to the format of your choice.
And this is why DRM is a Bad Thing. Seriously, would anyone buy paper books if their books were all destroyed when they moved to a new apartment? Obviously not. So why do we tolerate a system that destroys our books when we move to a new reading device?
DRM is to rights management like DDT is to pest management.
Filesystems manage files. Calibre manages books. Let calibre do what it's there for, and don't go peeking up its skirt. It'll slap you. ~ ~ (explanation here