The initial array from the file contains 200k records but they are not being added to the hash...

Then your data isn't arranged as you said it is.

The %array2 contains a single line: key=""

Hashes have elements, not lines.

and %array{$key} returns one record from array2

%array{$key} is a syntax error, there is no variable named "%array" in this discussion, and "array2" could refer to the array @array2 or the hash %array2.

The initial array from the file contains 200k records but they are not being added to the hash...

My code doesn't even try to add the 200k records of @array1 to the hash. It adds the 50k records of @array2.