Very interesting thread (IMHO).
Just a minor point as a start: Voynich should not be blamed for hiding the provenance of the MS. This was entirely due to the Society of Jesus and he was following their instructions.
In general, I have run into four types of 'loss of information', just from researching the history of the Voynich MS, or at least primarily.
1. Fires and other natural disasters
2. Thefts
3. MS mutilations (major and minor)
4. Things just disappear without a trace
For point 1, there are a number of well-known cases. For one, the Swedish war booty from the 30-years war, including lots of books and other treasures from Rudolphine Prague, was taken to Stockholm. A catalogue was made, the library went on fire and another catalogue was made, so there is a clear picture of the list of books that was lost. Here is a general article about this part of history from a perhaps unusual perspective (sorry in German):
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Another 'famous' fire was the Leuven library in WW2, but there are many more.
The case of the Galileo forgery is also associated with thefts from a library:
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and so is the case of the Vinland map:
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(search on the page for 'Ferraioli', but there are likely more detail on-line sources about this).
MS mutilations come in a variety of forms. Occasionally book dealers found it lucrative to sell manuscripts on a page by page basis. The sum total income was higher.
One of the web pages in JKP's contribution shows books from which pages have been removed. The Beinecke library has been a consistent target for this kind of mutilation and theft for some time, where a thief removed maps from books. This was a fairly well known collector, and someone may be able to dig up his name.
On a less destructive scale, some collectors preferred to rebind all their books and manuscripts. With this, all provenance information that was written on the old covers was lost. A typical case is is the bibliotheca Rossiana. See for example in this German article:
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(page 6).
This also happened with the Voynich MS, which was rebound by the Jesuits. There may well have been useful provenance information on the previous cover. Now we just have the Tepenec ownership that was written on the first folio.
Case of collections just disappearing are also quite frequent. One unfortunate example for the history of the Voynich MS is the library of Joh.Marcus Marci, which may well have included the letters he received from Kircher, other books he inherited from Barschius, some of which may even trace back to Tepenec.
This library was inherited by his son, who deposited it in the Augustinian monastery of Zahan (now Sagan in Silezia). It just disappeared from there.