A couple more comments that may help if you are still following.
I have been looking a bit more into it and see that ADE2.0 does not keep a single manifest.xml file (ADE1.7.2 does),
but rather keeps a set of .xml file in Documents\My Digital Editions\Manifest
That makes it easier to make sure ADE2.0 does not have any record of the loan previously,
by deleting any corresponding .xml files from that directory.
As your Manifest directory is empty, that does not appear to be the cause of your problem anyway.
You might find that you have multiple copies of the .acsm file as a result of multiple loans.
Make sure you are trying to use the correct (later) one to access the borrowed book.
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I've also been reminded of a bug in ADE2.0, where it cannot handle Overdrive library books when certain eReaders are plugged in.
This includes Sony PRS-350, and some other eReaders.
The failures are most peculiar when there is such an eReader plugged in.
One is that if you try to open an Overdrive library book on ADE with the reader plugged in,
ADE comes up with the message 'No record for this loan is found on this computer'.
This is without trying to do anything to do with the eReader, just trying to open the book on the computer.
Though this does not seem to relate exactly to the problems with you see trying to access re-borrowed books,
it does confuse things and could be somehow related????