Fact: Stephanus said in 1550 that the manuscripts in question were in the Royal Library in Paris.
Fact: The printer's note for Beza's edition said that the manuscripts in question were in the Royal Library in Paris.
Fact: The manuscripts are said to still reside in the Royal Library and no one has ever shown that they left.
Fact: Beza said in his 1556 preface that he had a copy from the library of Stephanus "collated as accurately as possible" (he doesn't mention manuscripts but the collation).
Fact: Beza said in his 1565 preface "In addition to all this came a copy from the library of our Stephanus, collated by Henri Stephanus" (he doesn't mention manuscripts but the collation)
To that we have the one you have focused on (or at least this is what I presume you are referring to):
Fact: Beza said in his 1582 edition "we collated these books...again with the various readings from the seventeen Greek books cited by Robert Stephanus".
There is only one way to interpret this information consistently. They can only all be true if Beza is referring to the collation as representative of the manuscripts. And if he believed that the collation and critical notes were representative of the manuscripts, then there was no need for him to consult the manuscripts personally but could sincerely talk about them as if he had. That's not dishonest, we do the same when we use the critical apparatus even though none of us personally saw the manuscripts behind it. This fits all the facts quite well and does no violence to any of Beza's words.
But for your claim to be true you have to:
- ignore the other five facts,
- assume that Stephanus and Beza's printer were lying or mistaken and that
- the manuscripts in question actually did somehow make it to Beza and
- The Papists in all their accusations against Protestants never bothered to claim that the Protestants stole their manuscripts,
- That Beza looked at them and either managed to smuggle them back into Papist-controlled Paris
- or that forgeries or other copies were put in their place and everyone covered it up,
- then Beza lost the manuscripts.
- And no one has ever seen them except for Beza.
All of those leaps of logic based on what you say must be the only interpretation of some of Beza's words; which interpretation doesn't match other things Beza and his printer said.