I have a few Phrags that are susceptible to rot, including some long petalled bessaea hybrids. I've made a few changes that appear to have helped considerably.
1. I put them in the highest air flow sections of the growing area. I keep them at the edges of my growing shelves on the sides that face the fans.
2. With the long petalled hybrids that have issues with rot, I don't let them sit in water. They never dry out completely, but are watered regularly and not allowed to sit with wet feet. In other words, they get the Paph treatment with respect to watering.
3. Keep them root bound. Use as small of a pot as possible and if possible use a rot resistant potting media that will allow these plants to stay in the same pot for a couple/few years.
Another thing I try to keep in mind is that P. besseae and at least some of the caudatum group don't appreciate hot temperatures. I grow indoors, but even then in the summer the grow room can get a bit toasty. One thing I do with lots of plants that might help with the temperature aspect is that I pot them up in plastic pots, then set those down into clay pots. The clay pots keep the potting mix from sitting in water and soak up the excess water. I assume there's some degree of evaporative cooling from growing this way, which in theory could be beneficial for plants that like cooler temperatures. Aside from plant preferences, cooler temperatures tend to retard the growth and virulence of pathogens like Erwinia, so even if cooler temps do nothing for the Phrags directly, they can still prove beneficial from a disease control perspective.
In years past, I relied heavily on rain water for my orchids, and I suspect that introduces a vector for infections to infiltrate the collection. Now that I live in an area with excellent tap water, it does seem like I've had less issue with things like Erwinia. However, my mind's not made up on this issue, it does seem plausible.
I've also seem some reduction rot/infections with a preventative Neem regimen and also with preventative inoculant application. In the past few years, the price of inoculants has come down and availability has increased. They each have their pros and cons. Neem is messy and I don't like the smell (since I grow indoors that's an important consideration), but it also helps reduce and prevent critters like spider mites. Granted, Phrags tend to be affected less by critters than other genera, but in a mixed collection that aspect can be helpful. Inoculants are quite varied, but tend to be more expensive than Neem and don't offer much in the way of protection from invertebrates. Additionally, some of them smell even worse than Neem. On the plus side, there are some inoculants with little or no smell, and most of them (at least in theory) are said to provide additional benefits above and beyond disease prevention. They also don't leave an oily residue all over the plants and equipment like Neem and horticultural oils do.
Finally, when you have infections in the collection, it's important to get rid of the infected material as quickly as possible and make sure to always practice good sanitation. Infected material should be moved away from and out of the growing area entirely. Gloves, hand washing, and clean tools are important. Surfaces should be sanitized. And if a plant is repeatedly infected, you may need to quarantine it and go nuclear with treatment (i.e. using physan, fungicides, antibiotics, repotting, etc).
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