I created a 2 layer beacon, got resistance, and when i was removing the second layer, i still had resistance even though the beacon only has 1 single functioning layer and should only give speed and haste. other effects might also have the same issue
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However, this issue is a Duplicate of MC-2440.
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Confirmed. I watched the timer for Jump Boost go down to 0:07 then glitch back up to 0:10 and repeat even though the second layer was completely removed from under the beacon.