Your assessment is on-the-money Bigkid. A parallel new branch could be an answer.
In some areas of such flooding the Chinese used interlocking steel sheets on either side of the roadbed, pumped out the water, and installed dry elevated fill. You will have vertical oscillation of track unless you have a solid base-and mud-pumping. Think "squish-squish". With every squish and passing of a train you lose stability.
AMTRAK produced a study on the degradation of roadbed on tbe NEC corridor due to mix-pumping in selected areas of track producing a predicative model based on weight, speed, and frequency of track use.
What I would like to see is what is called an "engineering economy study" of alternatives.
Can track super-saturated roadbed subject to mud-pumping be safely maintained?
Yes. But only with periodic reballasting. And constant monitoring of the stability. In the case of the high-traffic NEC, every two weeks.
A previous comment on "slow orders" is relevant.
We have to consider that a permanant restriction on train speed and weight and frequency would result in a reconstruction model of significantly less cost. Dedicated freight cars with six-wheel trucks would reduce the wear-and-tear. If there is a temporary repair how about some specially-constructed dedicated consists and engines that would be able to run with extremely light loadings? Supposing, instead of 80,000 pound cars on conventional trucks we had 30,000 pound cars on multiple trucks or six-wheel trucks? In other words light-weight low-damage trains?
New extremly light-load low-damage passenger and freight cars designed and built for dedicated service over track that cannot support existing equipment?
What would be the minimum tonnage and traffic that would maintain the viability of the community? Predicting maintenance costs of trackbed is related to this consideration. What minimum use could be projected without "the straw that breaks the camal's back".
You brought out another qualifying factor. The apparant alteration in climate in the area resulting in less cold weather. I am not going to say man-made, but it seems to be happening.
But we don't know how long the water levels will remain high. A significant unanswered question. Or if the flooded areas will freeze entirely, even with the cold weather coming on. Not to mention planning for future flooding. Installing culverts while you have high water levels on each side of the track is meaningless.
There is access by the port, albeit not for all year. The town could be resupplied with essentials such as propane for a limited lifestyle.
Deferring a decision until water levels recede seems reasonable.