I'm keen on building conservation, but not to the exclusion of all progress.
Track lowering has already been done, this was the work to clear Pendos. The line is already prone to flooding, do we really want to make that worse?
I agree sometimes buildings need to be brought down, however, appropriate procedures should be followed, not the approach of purposefully "accidentally" bringing them down with illegal and potentially dangerous methods, whether with a out-of-gauge train, arson, or the highways england approach of just covering everything in concrete. The fact that they aren't actually listed certainly makes the procedures easier.
Drainage (and flood walls if needed) could be improved. However, track lowering is only one of many options available in the toolkit of the railway, and deciding which is right will require detailed information of the line in question. It sounds like drainage improvements may be desirable regardless of whether the track gets lowered!
In any case, given these are undoubtedly differing bridges, a different approach or combination of approaches could be the right one for different bridges. What I am sure of is that the railway has the ability to electrify this line.
