This is long and detailed. If you need a TLDR version let me know and I'll write one up quick.
Doing a quick comparison of the PC 1975 Buffalo Div Track Chart, the Conrail 1978 Buffalo Div Track Chart, the Conrail 1999 Albany Div Track Chart, and the 2004 CSX Albany Division ETTs, I see the following changes (just focusing on crossovers and controlled sidings, not looking at every spur/IT etc):
Crossover directions are TT West. All changes unless otherwise noted occurred between 1978 and 1999 Conrail TCs.
Edit: Sorry, in rereading, I realized that about halfway through I inadvertently switched from "SS" to "CS" - these should be taken as the same meaning - signals control egress from ends of the sidings)
- CP 3/CP 296 (Belle Isle) - West end of SS and crossover 1->2 remains unchanged.
- CP 4/CP 300 (Warners) - Double Crossover 2->1/1->2 remains unchanged
- CP 5/CP 306 (Jordan) - Crossover 2->1 remains unchanged, East end of former SS off #1 is now dead-end spur leading to Jordan IT (In actuality I believe the Jordan IT has actually been abandoned now as well, but most recent document I have access to is 2004)
- CP 6/CP 308 (Jordan) - Crossover 1->2 remains unchanged, former Jordan SS to #1 removed.
- CP 7/CP 313 (Weedsport/N Port Byron) - Crossover 2->1/1->2 remains unchanged.
- CP 8/CP 320 (Seneca River) - Crossover 2->1 and East end of Savannah SS remain unchanged.
- CP 9/CP 323 (Savannah) - Crossover 1->2 and West end of Savannah SS remain unchanged.
- CP 10 & CP 11 (Clyde) - Crossover 2->1, Clyde SS, and Crossover 1->2 all removed between. Signals at CP 10 converted to 326 Autos (western bridge removed). Signals at CP 11 converted to 329 Autos, EB signals added to bridge, were previously on a bracket.
- CP 12/CP 334 (Lyons East) - Crossover 1->2 only, Lyons SS/Yard Lead from #1 remain unchanged.
- CP 13/CP 335 (Lyons West) - Crossover 2->1/1->2, Lyons SS/Yard Lead to #1 and Corning Secondary to #2 remain unchanged.
- CP 14 & CP 15 (Newark) - Crossover 2->1 (@ 14) and Crossover 1->2 (@ 15) Removed between. Newark SS removed, only lead to OMRR remains at former 14 w/no signals. Signals from both condensed to 341 Autos.
- CP 16/CP 349 (Palmyra) - Crossover 2->1/1->2 Remains unchanged.
- CP 17 (East of Wayneport) - Crossover 1->2 and east end of SS (what would've been a longer "Fallon's Siding" as CSX now calls it) removed. Fallon's truncated from MP 356 to MP 358 and uncontrolled on east end.
- CP 18/CP 359 (Wayneport) - Crossover 1->2, West end of Fallon to #2, Crossover 2->1, and #2 to West Shore (in TT Order) remain unchanged. #1 to CS (formerly extending to #3 beginning in Brighton) removed. Remains of CS existed as Fairport IT until recently, with the connection moved to MP361.
- CP 19/CP 362 (East Rochester) - Crossover 2->1/1->2 remains unchanged. Former crossovers between #1 and CS removed with CS mentioned above.
- CP 30/CP 367 (Brighton) - Brighton IT->2/2->1/1->SS/1->2/SS->Yard Crossovers all remain unchanged. As mentioned above the CS from Wayneport formerly met directly to the CS here, with a crossover from CS->1 (removed).
- CP 31/CP 369 (West end of Goodman Yard) - YL->CS/CS->1/1->2 Crossovers remain unchanged. CS continues west CP 373.
- CP 32 & CP 33 (Rochester) - Existed on #1/#2 only, Bracket signal at CP 33, removed between 1975 and 1979, possible old lead for station?
- CP 34 (Rochester) - Existed on #3/#4 only, connecting to "Old Line" between Plymouth and Canal streets, removed.
- CP 35/CP 373 (Rochester) - Crossovers 2->1/1->3(CS)/3->1/2->1 Remain unchanged. Former #4 main crossed to #3 removed. #3(CS) crossed to #4 Main (still existing as NCS westbound), Charlotte RT splits off this NCS here.
- No CP - Former #4 Main continues to MP 374.4, called "Pfaudler's" by CSX, where it converges back to #1, no main crossovers. #4 formerly continued as NCS to MP 378 (called "Outer Loop" by PC). Remains exist as "Pixley Siding" east of Coldwater.
- CP 36/CP 380 (Chili East) - Crossover 2->1, 1->Chili Siding remain unchanged.
- CP 37/CP 382 (Chili West) - Chili Siding->1, West Shore->2, Crossover 2->1/1->2, remain unchanged.
- CP 38 & CP 39 (Bergen) - 2->1, 1->CS, Bergen Siding, CS->1, 1->2 all removed. Signals converted to Auto 389 (tri-lights).
- CP 40/CP 393 (East of South Byron) - Crossovers 2->1/1->2 remain unchanged.
- CP 41/CP 402 (East Batavia) - DLWR->2, 2->1, 1->CS remain largely unchanged. Former Westbound Bracket signal replaced by Conrail with standard posts.
- CP 43/CP 408 (West Batavia) - CS->1, 1->2 remain unchanged.
- CP 44/CP 410 (Pembroke) - 2->1/1->2 Remain unchanged.
- CP 45 (Corfu) - 2->1, Corfu CS removed in entirety.
- CP 46/CP 417 (Crittenden) - Corfu CS removed as above, Crossover 1->2 remains.
- CP 47/CP 423 (Wende) - 2->1/1->2 remain unchanged.
- CP 46B/CP 429 (Depew) - 2->1/1->3/3->4/1->2 Remain unchanged, beginning of Buffalo Terminal Sub.
Only one change above, the lead in Rochester at CPs 32/33 (station?) was made between 1975 and 1978, all others occurred between 1978 and 1999. I could look at other TCs within this gap to find out more details, but that's a lot of large documents to load and browse through.
It is also, I feel, important to note that all sidings I listed as Controlled Sidings (CS) were shown with signals in both the PC 1975 and CR 1978 TCs. Another major change between 78 and 99 was that CR converted all these to non-controlled sidings (which I believe would have meant verbal permission from the DS to both occupy and leave the sidings). In addition to listing all as "NCS" instead of the previous "CS" both they and PC had used in previous TCs, the signals are visibly removed from them and in some cases other signals at the CPs were reconfigured (one strong example is CP 402 where the signals governing the Batavia Siding and the DLWR/Caledonia leads are removed entirely). Visual recon and indications from CSX documents indicate that they have returned basically all of these sidings (except where still noted as NCS above) back to controlled status originally via a large number of dwarf signals but notw even more obviously in that they now have replaced those dwarfs with full-height Vader signals.
1975 PC Buffalo TC
1978 CR Buffalo TC
1999 CR Albany TC
2004 CSX Albany ETT
Conrail TC List in case you wanted to explore more to determine more about when some of the changes were made, but you'll have to browse through the large documents, either Buffalo or Albany depending on the year, to find it, as well as learn how to read them (took me some time to fully figure out a few years back)