I'm not an expert on XSL-FO, but the answer to the question "can I use different stylesheets to process the same source document" is YES: one could say that's the whole point of XSLT!
You can also arrange that the two stylesheets share a lot of common code (two stylesheets A and B that import a common module C), or you can use the same stylesheet with different parameters.
The only time this is a bit difficult is if you are controlling XSLT evaluation using the <?xml-stylesheet?> processing instruction.
How are you invoking the transformation?
Author, XSLT Programmer's Reference and XPath 2.0 Programmer's Reference