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Until recently I could not make out the first word of that recommendation, but I now see that it is Sphi with a line over it; that is, the word Sphinx in abbreviated form. Marci is not short of space on the page and the abbreviation cannot be intended to deceive. It is surely intended as a minor jibe at Barschius and his Big Secrets. In the last but one paragraph we read sile with a line over it (there is another example in the third from last line of Marci's letter of 9 November 1643). This must be silenda or silentia, 'matters for silence', and could easily be a reference to censorship (you don't keep secrets by talking about them).
The word schaedata is not in classical dictionaries. It is grammatically singular and plainly means an item of writing.
The three sentences tell us two things. One is that Barschius has dragooned Marci into forwarding (and perhaps doing the work on) yet another facsimile of the manuscript. The other is that Kircher wants to know who Barschius is and Marci reassures him that Barschius is a vir optimus (like vir bonus this seems to have social connotations) and acts from the purest of motives.
The heliotrope in the next paragraph cannot have anything to do with the alleged sunflower in the Voynich manuscript. The reference is to something Kircher knew about and Marci did not. 'Our friendship' means that of Marci and Kircher: Marci would not casually have claimed the friendship of his monarch. The emperor in question is Ferdinand III (born 1608, reigned 1637-1657).
The word succulatum is not in classical dictionaries: presumably it was a fluid used in printing.