Ok, here is a little bit of information about how RCT2 handles files. There are programming tricks you can do that break these rules, but for now just obey these rules:
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Do NOT delete the files in the top RCT2 directory called rct2.exe, readme.txt, or manual.pdf if they exist (these are RCT2 program files).

Do NOT delete ANY files in the DATA directory (these are RCT2 system files).

Do NOT delete the file called 001 (IF it exists) in the LANDSCAPES directory. You CAN delete any other files in this directory if desired (this directory is just a convenient holding pen for files you may wish to use in the Scenario Editor).

Do NOT delete any of the default RCT2 *.dat files in the OBJDATA directory (some of them are used as part of the opening screen animation). Any other *.dat file is a User Created (or Chris Sawyer or Wacky Worlds) object file, and they CAN be removed. 
Scenario files that have custom objects EMBEDDED into them (such as all our UCES "*.SC6" files) will never have a problem running (all objects will properly show up under the scenery tabs) even should a file the scenario uses not be in the "OBJDATA" directory when the scenario is launched. This is because the embedded scenario itself will self-populate the directory with any missing "*.dat" FILENAMES (the entire object file is stored as part of the scenario computer code itself, which is why these embedded scenario files are so big). 
Save game (*.SV6) files on the other hand DO require that ALL the necessary custom objects are installed in the OBJDATA directory before they will load (actually the save game checks for the custom objects FILENAME, so don't rename a custom object file that has been used in a scenario). Also, the only way to get an object onto the Scenario Editor object pick list is to have the custom object sitting in the OBJDATA directory prior to launching the Scenario Editor.

Do NOT delete the files called tracks.idx in the TRACKS directory. You CAN delete any other files in this directory if desired (*.TD6 files are just saved track designs). The tracks.idx file will automatically re-index itself as track design files are added, removed, or RENAMED (and also note that unlike "*.dat" object files, "*.TD6" files have nothing to do with scenario funtioning).
Note that unlike the Scenario (*.SC6) files, the *.TD6 filename (minus the .TD6 extension) IS the name that appears in the track design pick list. Very long filenames will clearly show in their entirety under the picture of the track design in the pick list. Do note that although the list column in the pick list will truncate the end of very long ride names (due to "textfield length limits), the truncation will have NO effect on your ability to select or modify the track design.

You CAN delete ANY files from the SCENARIOS directory if desired (even if all scenarios are removed, you can still launch an RCT2 game session by either running a Saved Game or running one of the tutorial scenarios).
Note that unlike with Track (*.TD6) files, the *.SC6 FILENAME has NO effect on the name that appears in the Scenario Pick List (and you can have multiple IDENTICAL scenario names appear on the Pick List if these names are associated with different *.SC6 filenames). As can be seen on the last page of the Scenario Editor, the Pick List Scenario Name is as customizable as any other Scenario setting (such as starting money), and does not have to be the same as the filename (and, like starting money, can only be changed if the scenario is run back through the Scenario Editor).

You CAN delete ANY files from the SAVED GAMES directory if desired (*.SV6 files are just saved games). If you delete the file called scores.dat, RCT2 will just recreate a default one.
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ABOUT SCENARIO PROGRESS:

RCT2 keeps track of scenario progress by updating the scores.dat file in the SAVED GAMES directory. [Please note that if a file with this name is missing from this directory, RCT2 when launched will create a new default file that will NOT have any saved game progress information]. 

The scores.dat file can be replaced with another scores.dat file which reflects different scenario progress (i.e., you can regularly backup this file and then restore your scenario progress to an older level of progress [and although I havent tested it, you should theoretically also be able to install a scores.dat file with different scenario progress information from a different computer that is running RCT2]). 

An interesting thing about the scores.dat file is that it keeps track of progress information from specific scenario (*.SC6) FILENAME that you may have physically removed from the SCENARIOS directory. 

For example; lets say you won the scenario Electric Fields. You will note a checkmark next to the Scenario in the games Pick List. Now close RCT2 and physically remove the file Electric Fields.SC6 from the Scenarios directory. When you restart RCT2, Electric Fields will no longer appear in the Scenarios Pick List. Now close RCT2 and put the Electric Fields.SC6 file back into the SCENARIOS directory. When you restart RCT2, not only will Electric Fields appear on the Scenario Pick List, but it will STILL have the checkmark next to it (indicating the scenario was already won).

Another interesting thing about the "scores.dat" file is that it tracks ONLY the specific "*.SC6" FILENAME. It does NOT matter what data has been changed. 

So, to expand the above example; you could delete the finished "Electric Fields.SC6" file and rename a different file (even in a different catagory, such as for example "Ghost Town.SC6") as "Electric Fields.SC6". Now the checkmark will appear next to the renamed "Ghost Town.SC6" file Ghost Town listing in the Scenario Pick List. 

