Where the error's exactly from:
https://github.com/UXR7b/csgo2018lea...ystem.cpp#L319 (and more lines at below)
So according to it you're probably running out of a fixed space to map key strings to key symbols (haven't looked into the system, pure guess).
However, there's an internal function
KeyValues::SetUseGrowableStringTable(bool), easy to tell that it can turn to a growable vector for the mapping.
Should be handy for you to access it through SM in server lib, but the effects remain unknown.
But my question is how would you run into messing with such a number of files?
Edit: Looks like if you'd like to use the growable table
under its limitations, you have to find a way to call the function
before all I/O to KeyValueSystem (perhaps via valve plugins).