To relieve the immediate pain, first thing I would do is identifiying the use of various hash keys among the file set of the application in question and move the shared keys into *.pm files which export those constants, to be used by those files using the constants - "divide et impera" - much like C header files. That would help with the 'single file issue', but it might introduce more complexity at another level.

Next you could consider restricting the key set of a hash via Hash::Util, or using accessors, probably as lvalue subs, e.g.

sub this_id :lvalue {
    $_[0]->{this_id} = $_[1] if @_ > 1;
    $_[0]->{this_id};
}
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Then you can say

    $r->thisid = 10;
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but for this notation, $r has to be blessed into the package this constant lvalue sub is defined in.

update: corrected sub