Methylene blue can help for ammonia damaged gills on first arrival - it's the first stage in BlueLife's Safety Stop and is generally not a negative.
Methylene Blue What It Treats – Healing agent which treats ammonia burn, abrasions, cuts. Mild antiparasitic/antibacterial properties. Will possibly detoxify a fish that has been exposed to cyanide poisoning. Probably one of the best “first response” treatments for a sick fish. How To Treat –...
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I am no expert here, but in the past, making sure the acclimation bucket gets a reasonable amount of air (not so much that it pushes a fish around if it can't stay upright), a small heater (I use those 5W always on types), and a few drops of an ammonia detoxifier have been helpful for me in the past for a several hours long but reasonably fast drip drip acclimation. Had a couple fish come in not being able to keep upright who ended up making it - not 100% by any means and I'm not a vet, but I feel like it's better practice than a lot of acclimation recommendations.
Keeping stress to a minimum (including bright lights or active bucketmates) at least helps not make it worse, but my approach has been that the ammonia and oxygen issues must be dealt with immediately, whereas the temperature and water quality issues should be dealt with slowly to minimize additional stress.