Joe,

The "transcripts," as I've understood it, are the original manuscripts.

The renditions of chanties collected in these manuscripts were used by Sharp to make up the versions he (Sharp) presented in the 1914 work you mentioned, as well as one or more (can't remember) that went into RR Terry's collection. Not all of the collected Short renditions (i.e. as represented in the manuscripts) were used for those collections, though most were. It is important to note, too, that they were often used as part of a synthesis of different individual's renditions to create the published version. In practical terms, Sharp, for example, might have presented the melody and a verse sung by Joe Blow Seaman and then tacked on a verse or two from the Short rendition.

According to my analysis, the Short chanty items in the manuscripts (i.e. judging from the content of the CDs) that did not make it into Sharp's English Folk-Chanteys or into Terry's work are:

NEW YORK GIRLS
SACRAMENTO
WHISKEY JOHNNY
DIXIE'S LAND
CLEAR THE TRACK
GOODBYE FARE YE WELL
LOWLANDS AWAY
PADDY ON THE RAILWAY
REUBEN RANZO
ROSABELLA
(The titles are generic ones I use...I can't be bother just now to locate Sharp's idiosyncratic titles.)

So, one will find notations of most of the other chanties from the CDs in English Folk-Chanteys. Incidentally, in some cases, Stan Hugill also reproduced versions presented by Sharp, if they were appreciably different from those familiar to him.

FWIW I have noticed that English Folk-Chanteys was not much utilized (relatively speaking) by the early Revival singers in constructing their renditions. One good, possible reason, is that the versions it contains did not supply enough verses for a performance. RR Terry, Joanna Colcord, etc, remedied this by combining verses from multiple sources, and so their collection were more handy. The effect of this is that to people steeped in particular established Revival "versions," renditions based in the John Short manuscripts sound "different/new"--regardless of whether they are being pulled from the archive or whether they have been in print for almost 100 years.