Very interesting question! There are no rules about this one! This is a situation where you consider the needs of the reader along with the requirements of the person requesting the braille.
Here is a suggestion: Give each separate pdf a letter. So the first one is A with pages A1-A3; the 2nd is B with pages B1-B31, and so on. On the TN page you can explain that you've added the letters to separate the pdf's - and identify which pdf is which letter (by title?). That makes the print page numbering much more clear and easy to follow for the reader...imagine trying to find the correct page 1 among 7 different pdfs! Braille pages can still be consecutive within the volume. Your Title page would then reflect pages A1-A3 and B1-bB31, etc.
I do realize that from the title page the reader won't know which pdf is which - but once they understand your system, it should work. Be sure to make your Table of Contents numbers (are you doing one? this would be a good place for a transcriber-generated Contents for the reader's benefit) match whatever you've decided...it's probably a quicker way for the reader to find what they are looking for.
Again, just a suggestion. Let me know what you decide!