Jamie,
Taking that dissertation from the top:
At least a fair proportions of the staff at Jena did not "escape" to the west; they were held at gunpoint and the GIs were ordered to ask them either to go walking, or be in a box. "Kidnapped" might be a better term.
The name "Carl Zeiss Jena" did not come into being after the division of Germany. The company was called Carl Zeiss Optical Works, and following the tradition of the time, also marked the location, as in the Schneider company is not called "Schneider Kreuznach", it is Schneider, at the town of Bad Kreuznach. Naturally, the new Zeiss optical establishment in the American Zone was no longer in Jena so it was not entitled to mark its products "Carl Zeiss Jena".
The inverted telephoto lens Flektogon was a post-war Jena design and the appellation was never used by Oberkochen, thus there had never been a need to abbreviate it. On my desk is a M42-mount "export version" 35mm/2.8 Flektogon, first automatic diaphragm version, marked "Jena" (rather than "aus Jena") and the Flektogon name is spelt out in full.
While it is true that many legacy lens designs made by Oberkochen and Jena were similar, if not identical, design directions started to diverge fairly early on. The Biometer is a five-element version of the Double-Gauss lens but more akin to the Schneider Xenotar than the Oberkochen Planar for the Rolleiflex.
In the UK, and perhaps some other countries, a somewhat Solomonic approach was given to both Oberkochen and Jena where there was no need for either of them to disguise their products in any way. For many years the Sonnar sold in the UK were indeed marked as such, and that also applied to other lenses as well, although sporatically some "abbreviated" examples were distributed, but still bearing the full Carl Zeiss Jena markings.
Carl Zeiss Jena was never absorbed into VEB Pentacon; it remained an independent company until 1985 where it actually bought out Pentacon and various other photographic equipment manufacturers. In the late 60s or early 70s Pentacon sort of nudged it way to acquire Ihagee which, even after the partitioning of Germany, was still Dutch-owned, even though it is more on paper than in reality.
While most of the "consumer" lenses by Jena were made for Praktica, thus for a very long period, in M42 mount, it was also a major supplier of lenses for Exaktas, and also the Praktisix/Pentacon 6 series, let alone less long-lived lines such as Praktina and Werra. But it tried to stay as a supplier of lenses to all camera manufacturers too: not long after the partitioning of Germany Jena not only supplied to local makers such as Belca (the original Balda before it started up again in Bunde), Bentzin (for the Primarflex models), Kochmann (Reflex-Korelle and the later Meister-Korelle) but also continued to make large format lenses such as the Tessar in a variety of focal lengths, the manufacture of which continued until reunification. Overseas, Jena did supply Bronica with lenses for a very short period and these lenses are becoming rather scarce nowadays due to collectors interest.
Way back in the 1880s, the Zeiss designer Ernst Abbe discovered that new types of optical glasses were required to effect further correction of optical aberrations and to cut a long story short, Otto Schott founded a glass company in Jena to develop new types of glasses which were supplied to Zeiss. With the partition of Germany, a new Schott glass factory was established in Mainz and that was where Oberkochen sourced its optical glass, rather than the original one. Of course, if the recipes are identical the glass would be the same no matter where the factory is.
While Jena camera lenses covered a huge variety, to consider those only for 35mm SLR would still be more than just M42 screw mount. But if later, multi-coated lenses are what we are interested in, we have to consider those made for the B-series Prakticas as well, in bayonet mount.
The appellation "Prakticar" had appeared three times, in different periods, and in different contexts. At first it appeared probably before the war on low-cost lenses as if it is an "own-brand" lens, the existance of such has only recently been confirmed. Then in the seventies, the British arm of Jena, who also represented Sigma (among others) launched a series of Sigma-sourced lenses with the blanket-label of Prakticar which were of pure Sigma design, and many of them equipped with the electric indexing contacts required by LLC/VLC/PLC/EE series. Finally, with the advent of the B-series, first shown at the 1978 photokina and sold from 1980, all the lenses, no matter where they were sourced, were all given the name "Prakticar" even though a large proportion of them were existing Sonnar, Flektogon, etc. put into the new bayonet mount, with the rest being completely new designs.
The M42 mount did not originate with Pentacon: it was first made during the war years at Zeiss Ikon (in Dresden, of course) but never released on a product. After the war, the chief designer at Zeiss Ikon Dresden, Wilhelm Winzenberg, finished Hubert Nerwin's war-time project of converting the Contax into an SLR with eye-level viewing by redesigning the Contax from the ground up, and elimated the vertical shutter which was the inconquerable stumbling block which thwarted Nerwin by using a horizonta shutter. The need for a larger and shallower lens mount induced Winzenberg to use th M42 mount, and the resultant camera, the Contax S, was released in 1949. In the mid 1950s KW, maker of Praktiflex cameras which used a smaller screw mount, bought out Zeiss Ikon Dresden; this also led to the adoption of the M42 mount on KW's cameras, thus the Praktica with M42 was the result.
Hope this is of some interest.