Alderton Tunnel is the shorter one, just east of Chipping Sodbury Tunnel, which has been nothing but trouble due to flooding ever since the day that cheapskate GWR engineer Grierson had it designed and dug around 1900, well after basic railway engineering principles were understood. This is north of the better known Box Tunnel, by Brunel 60 years beforehand, through the same ridge of the Cotswolds - which I don't recall has ever had flooding issues.
We know what the problem at Chipping Sodury Tunnel is. The size of the drain under the tracks through the tunnel is not the problem (which is supplemented by an additional pipe fed by pumps). The problem is that the amount of water allowed by the Enviroment Agency into the stream (that feeds into the nearby River Frome) is limited to prevent flooding of local properties.
The 'duck pond' that Network Rail built was never going to be big enouth to handle the vast amount of water that comes from the tunnel.
It should be noted that even in the middle of summer, there are very wet parts in Chipping Sodbury tunnel. I've walked this tunnel far too many times...
By comparason, Box Tunnel is a dry tunnel. In fact, it's a very dry tunnel. Having walked through it, there are very few wet spots. However, there is a river directly under the railway at one point. You can hear the water!
I can't speak about the current situation, but the amount of resources was cut in 2010/2011 during the phase 2B/C reorganisation. The relevant engineering department was reduced in size (over the years after this, in some areas, the company did consult in some extra posts). This was on top of the reduced amount of maintance of drainage systems that had taken place since BR was privatised.
I've seen numerous track side drainage channels choked up with weeds, debris, mud, spent ballast etc.
Similarly, I've seen plenty of catch pits (drainage pits) where the covers have been dislogdged and ballast has fallen in partly blocking them, or grating/metal bar type covers have been used, and ballast from ballast trains or ballast regulators has been spread on top of them (not deliberately, but even so, it doesn't help), with large amounts falling through into the pit, again partly blocking them.
The sad fact is, that maintaining the drainage systems is a very low priority. Despite problems being reported, in many cases, nothing gets done for many years until there are repetitive days of train delays.
Ultimately we have a Victorian railway built to Victorian engineering norms.
Those norms are unlikely to be adequate for the challenges of the anthropocene, which is apparently upon us.
If you want to avoid such closures becoming more common a lot of money would have to be spent and a lot of infrastructure replaced.
It would help if the existing drainage systems were properly maintained. Climate change has been known about for over forty years. Okay, so predictions of increased rain fall, or large amounts of rain fall over a short duration are more recent. Regardless, the railway has done very little preparation.
It's not exactly rock science to work out that in order for the drains to cope with a greater amount of water, both the pipes, ditches, channels and the outfalls, streams etc that they flow into have to be increased in their capacity. This is basic engineering.
The real answer is that the powers that be are likely choosing not to spend the money on this.