The Book Switch Theory

[asteckley]

Anyway, the year 1604 is already explained on the web page. Note also that the 4 in the number and the 4 in the year are in quite different hands. 

This doesn't explain what I pointed out at all though. I think what you might be trying to say, without simply saying it, is that the librarian who wrote down that he donated the book in 1604 erroneously made that assumption because he saw the year 1604 written on the same page as the signature in the book. (Even though he would have been conflating the donation date with the signature date.) He was in error though because that 1604 was part of the stroked out previous owner whereas our Jakob actually wrote his signature on that page much later -- after 1608. Is that what you are trying to say?

That would still not explain the mixed up sequence numbers though.  You seem to be suggesting that the idea of "sequence numbers" being assigned in the natural order of our Arabic numbering system is merely a bad "assumption" on our part.  And  that that assumption needs to be reconsidered entirely because such an assumption lacks any evidence, and because these records do not otherwise make any sense. Is that what you are suggesting?  
OR...
Do you have a more reasonable explanation for the problem of the sequence numbers?