After discovering that the convert to PDF option in Calibre creates pdf files fully rasterized into 300+ megs of non-text selectable monsters

, I decided to find try a different way to convert to PDF. After viewing the epub or mobi in Calibre's internal viewer and choosing to print to "Acrobat PDF" I get 10 meg files with selectable text.

The problem I'm running into now is how to merge those files back into Calibre. I could just replace the larger meg files with the ones I've created, but for future books where I haven't used Calibre's convert to PDF option, I was looking for a better solution.
Right now what I've ended up doing is creating a new folder, moving all the book formats out of where calibre has them stored them, add my pdf file, delete the book from calibre and then re-import everything. Is there a quicker drag-n-drop solution I'm missing?
This program is amazing and it just gets better every day. I don't know what I'd do without it!