Seems $1 was reset after every matching.

Correct. The pragma use warnings would tell you:

Use of uninitialized value $1 in substitution iterator at...
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which indicates that $1 is undef, because nothing has been captured in the current substitution. Easily fixed by adding parentheses to capture the text you want to keep:

$ou =~ s/^\s*#\s*(PATH=.*\$NAS_DB\/bin.*)$/$1/;
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Hope that helps,