Not sure what is your scenario of hydrotesting the flanges, but leakage of any kind under any circumstances is NOT allowed according ASME B31.3
I my opinion, all flanges and joints previously hydrotested per ASME B31.3 and removed from the test stand then packaged and reinstalled at the plants, those flanges still need to go through field testing to verify tightness of every flanged joints even though paragraph 345.2.3(b) does not require flanged joints to be leak tested again.
The entire system does not have to go through the hydrotest again, but it at least be tested with inert gas (Air or Nitrogen) to ensure that they are leak tight.
I would be hard pressed if someone calls for any leakage allowance in flange connections. All flanged joints leakage in any facilities in the world has been contributed by flanged components. Many articles and lessons learned also document this subject.