Missing folios

[Jorge_Stolfi]

I suspect that folios 12 and 74 were cut out first, perhaps sent to Prague to Rome

The only person who could have done that was Baresch himself.   I don't see why Marci would have sent Kircher two pages before sending the whole book.   

However, in his You are not allowed to view links. Register or Login to view., Baresch says that he previously had sent copies of the pages, and said that Father Moretus could bear witness that the copies were faithful:

And so I ordered a certain old book to be transcribed in part, with the writing closely imitated (the bearer of this letter will inform you that he saw it with his own eyes). A year and a half ago I sent that writing to your Reverence. [...] It did not seem advisable to commit the book itself to a journey so long and full of perils. I could only suppose from the fact that I have had no word of the matter after all this time that the previous consignment did not reach Rome. I had therefore just decided to repeat the exercise when the above Father Moretus informed me to my great pleasure that it had ended up in the City. It would be an even greater pleasure if the said book could be opened by your Reverence’s aid, and make all men of quality co-owners of whatever good it contains. [...] I should be forever in your debt, not only for what the work contains but also for whatever it will make possible. I here append a line or two of the unknown script to revive your memory of it, having previously sent a whole file of similar characters.

Traducta itaque ali qua parte, scriptura imitata simili, ex libro quodam uetusto (cuius ocularis inspector, et informator erit praesentium lator) scripturam eam direxi ad Vestram Reuerendam ante sesqualterum annum, [...], librum enim ipsum itineri longinquo, periculis pleno committere, consul
tum non est: Siquidem etiam illud, quod proxima uice missum fuit, Romam non peruenit, ut ex eo colligo, quod tanto tractu temporis, nihil de hoc re scriptum intellexi. Quapropter altera more duxi repetendum, quod in Urbe feliciter appulisse, supradictus Pater Moretus mihi retulit, de quo uehementer gavisus sum, magisque gaudebo, si praedictus liber ope Vestrae Reverendae reclusus fuerit, ut eius, quod in se boni habet, boni possint esse participes [...]Pro quo ei obligatus ero, non tantum illo, quod opus illud continet, sed etiam quicquid aliud erit possibile. Adiungo hic aliquot lineas scripturae ignotae, ad revocandum in memoriam, ante missam similium characterum scriptionem.

So either he sent the real pages later, with a third letter; or it seems more likely that the pages were removed  by someone else while the book was in Rome.  

Or by Wilfrid, before he went public with the book...

All the best, --stolfi