Thanks again Harry, and Krystian.
In fact I ditched the SD card which came with the Cybook some time ago, and have been happily using a 1Gb AMicroe card which I formatted to Fat32.
The plot thickens.
After thinking about it overnight I tried another experiment. As I mentioned earlier I had thoroughly checked the 1Gb SD card's file system, but could not get it to work.
I tried again this afternoon with the SD card in the Cybook, and it still would not work with the Mobipocket reader on the Cybook.
Then I attached the Cybook to the computer, still with the 1Gb card, and used the Mobipocket Desktop reader to read the same book file. With the Mobibipocket Desktop reader I could resume from where I had stopped, and could set and remove bookmarks.
That is, the only difference is the version of the reader I was using.
This seems to weigh against Krystian's suggestion about Linux not writing anything to the SD card when the filesystem is broken - same file, same card; it worked with one reader and not the other.
I understand that there are differences between the two Mobipocket versions, and that the version on the Cybook is a 'cut down' version of the one for desktops; is this correct? Is it possible that there was a minor flaw in the ebook file which the Desktop reader can cope with but the Cybook reader can't?
But that would not explain why I have got the ebook file to run as expected on another SD card, a SanDisk 2Gb card using the Cybook reader.
I think I will use the SanDisk card and repopulate it from the backups.