What does this mean? And why can't I start from where I was?

Because updating AEoD versions (or the map set was modified) consequently means it cannot match the same data it was saved to in comparison with what you are currently using.

Aka goodbye saved games. You'll have to make another saved game.

This means that you whatever you're loading, is not the same as how it was saved.

This could be because of the following:
-Using a different SVN version of the engine
-Files were modified
-Running files in different order

For the latter, "zdoom.exe -file AEoD.pk3 AEoDdat.pk3" is not the same as "zdoom.exe -file AEoDdat.pk3 AEoD.pk3" for save-load purposes. And if you're running something else with aeod, that one adds to the equation

Ah, dang. Well, hopefully I can fix this. Thanks for the help, guys! Very fast replies.