The one that HAS been set (the always use tick box in Open With properties) in the OS.
Double click on a PDF in Explorer... What opens the file, is what Calibre will use.
Don't want Calibre to use that one? Get and configure the 'Open With' plugin to choose the one you want.
you can add lines so there is an entry choice for each that you have:
A PDF
B PDF
C PDF