For the currrent excercise, I would choose:
a. Do we treat them separately and record both/all of them.
So - using the example of Bolivia's "Copacabana village" I am presuming that, when finding similar examples of T List entries which have been removed and replaced by something rather different/bigger we should register the site as originally described in the "Formerly on the T List" category on the basis that it is different enough from the later T List entry.
However it sometimes ought to be possible to link the ealiers site to the later directly. For instance - where is it possible to access UNESCO's Reference Number, this gives a useful linking factor. So, to use the Maes Howe example raised by Euloroo above,
a. In 1989 Ref No 514 "Maes Howe and Brogar" was deferred (Yes it WAS 1989!!)
b. In 1999 Ref No 514 Rev "Heart of Neolithic Orkney" was inscribed covering a bigger number of sites
In my view it is incorrect to record the original site as having "Formerly been on UKs T List". Rather the history of the inscribed site should cover the history as the SAME site as
1989 Nominated and deferred on recommendation of the Bureau as "Maes Howe and Brogar" for extension and increased protection
1989 On T List as "Mainland Orkney"
1999 Inscribed as "Heart of Neolithic Orkney" with 4 locations
In fact if you look at the T List Documentation for 2000 it shows "Heart of Mainland Orkney *"
where "* = Site has been inscribed on WH List" proving the linear connection!
However, where we are not sure that a current inscription or T List entry is directly linked by ID or other reason to an earlier T List entry it seems better (in terms of providing "useful" information etc) to err on the side of putting potentially extra entries under the "Former T List" grouping. BUT it would seem worthwhile to try to identify the linkage which may not always be clear from the title unless one is an expert in the country involved (as in the case of "Copacabana Village" and "Sacred Titicaca Lake".) In the description for Copacabana Village it would seem easy to privide a link to the T List entry for the lake and to state "Now included in Sacred Titicaca Lake" site. Similarly the Sacred Titicaca Lake description could easily include a link to the village and text "Includes Copacabana Village" (and if it were to include several former T List entries there would just be several links).
In the light of this I will add "Chittorgarh Fort" to the list of "Sites Formerly on the T List" of India. Yesterday I didn't do so on the basis that it eventually got inscribed as part of the "Hill Forts of Rajasthan". However the linkage here was not "continuous" and it seems worth having Chittorgarh separately identified with text to the effect that it eventually gained inscription as part of the Hill forts -with a link to that site.