Why a fallow period will sometimes fail

We've all seen claims of ich, velvet, etc. returning after a 76 day fallow period. (For anyone wondering what a fallow period means click here: https://www.reef2reef.com/threads/fallow-periods-going-fishless.190324/)

Oftentimes, a fallow period failure is due to human error: The sick fish weren't treated long enough or the treatment itself wasn't done properly, cross contamination via wet hands or equipment, aerosol transmission (more info). It is also possible that undiscovered strains of ich (and other diseases) exist; ones with a prolonged life cycle that exceeds what we know to be true from scientific research. However, there is also this possibility to consider:

Dormancy induced by a hypoxic environment in tomonts of Cryptocaryon irritans, a parasitic ciliate of marine teleosts

Abstract
We incubated tomonts of Cryptocaryon irritans in a hypoxic seawater environment (1.4–1.7 mg/L O2) (low dissolved oxygen; DO) and examined their development using a acetocarmine whole-mount staining method we developed for nuclear staining. They showed little development and stayed in the dormant phase in the hypoxic environment. When transferred into the hypoxic environment after incubation in an oxic environment (air-saturated, 8.7–8.9 mg/L O2) for 1–4 days, their development stopped in 1 day. However, when dormant tomonts generated in the hypoxic environment were transferred to the oxic environment, they resumed development and released theronts. These results indicate that tomonts can become dormant when exposed to a hypoxic environment, but can resume development when exposed to an oxic environment at any developmental stage. When exposed to the oxic environment, tomonts recovered from 1-month dormancy and released as many theronts as control tomonts constantly incubated in the oxic environment. The infectivity of theronts from the recovered tomonts was similar to the control tomonts. Thermoclines prevent oxygen-rich surface seawater from reaching the bottom of water column and create a hypoxic sea floor environment in summer; these thermoclines are broken down in autumn or after typhoons. The long-term viability of dormant tomonts in hypoxic environments may be a key factor in the autumn outbreaks of cryptocaryoniasis in floating net cages in temperate waters.

Highlights from the study:

This study demonstrates that tomonts of Cryptocaryon irritans become dormant in hypoxic environments.
Dormant tomonts resume development in oxic environments at any developmental stages.
We examined tomont viability following variable sequences of oxic and hypoxic conditions.
Dormancy in hypoxic environments may be key to the autumn outbreaks of cryptocaryoniasis in floating net cages in temperate waters.

So what does this mean for us and our fallow aquariums? Primarily, the study showed that an ich tomont (the "egg stage" which encysts to corals, inverts, rocks, etc.) can go dormant if the protomont crawls into a hypoxic (low oxygen) environment or anaerobic (no oxygen) region of your DT just before encysting. Examples of this include under your sand bed (especially a DSB), inside a non-porous rock, any "no flow" region of a canister or other aquarium filter. The study also demonstrated that once returned to an oxygen rich environment, these once dormant tomonts resumed their development and released theronts (free swimmers which seek out fish to infect.) How long can it take for a dormant tomont in a hypoxic environment to suddenly be exposed to an oxic (oxygen rich) environment? The world may never know?!

So what can you do to eliminate low oxygen areas of your DT during a fallow period?

Take any canister or enclosed filters offline, and sterilize them with bleach. Without fish to foul the water, your DT will be fine with just rock/sand for filtration and good water circulation.
Speaking of circulation, crank up those pumps for maximum flow & gas exchange throughout the aquarium. (Don't forget to add a pump down in the sump.)
Blow out your rocks (using a powerhead) and vacuum the sand during water changes whilst going fallow. This will "stir things up" and provide free oxygen to those areas.

How can I setup my Display Tank to be "hypoxic proof" just in case I ever have to go fallow?

Only use filtration with an open top (like a sump), and avoid canister filters and other filters which may contain anaerobic regions. If needed, take these offline if ever having to go fallow.
Use just a light layer of sand; the deeper it is the more likely tomonts can get "trapped" down under there.
Never have sand out of reach (i.e. under a rock) in case you need to vacuum it during a fallow period.
Only use very porous rock which will allow plenty of flow (and oxygen) to pass through.

More information on Marine Ich (Cryptocaryon irritans) can be found here: https://www.reef2reef.com/threads/ich-cryptocaryon-irritans.191226/