$REPO_HASH {$gqueried_repo} {REPO_BRANCHES} = @branch_list  ;
  # Does not do what you apparently think it does
  # The result of the assignment above is the number of elements in @b
+ranch_list
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What I think you meant:

$REPO_HASH {$gqueried_repo} {REPO_BRANCHES} = \@branch_list;
   #Note: Added "\", which makes it a REF to the array
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You can unwind the HOHOA using:

  for my $k (@{ $REPO_HASH {$gqueried_repo} {REPO_BRANCHES} }){
     # Process one item of the array in $k
  }
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