Since you haven't posted any code, I am forced to make all a few assumptions about what you are trying to do. So if I don't answer your question, I hope you'll understand.

First of all, a blob is a binary large object. If the creator of the database did their work correctly, the entire contents of the PDF file should be present in the blob (no "conversion" requried). Indeed it would seem that the challenge you face is to NOT CHANGE the binary data when your program is handling it. You must take care to not introduce unwanted newlines and such. You should really look at the perlfunc:syswrite method for writing the resultant PDF file.

As for accessing the data, I don't see a CPAN module for DBISAM, but you could always use ODBC to retrieve the blob. Good luck.