The industry's position, as per condition 32.1 of the National Rail Conditions of Travel (NRCoT), is that Delay Repay is calculated based on the timetable advertised on the day of travel, which will have been amended since you booked to reflect the closure. That will certainly be the way that any claim you submit will be calculated and paid out (or not) at the first instance.
I have significant doubts as to the enforceability of the relevant clause in condition 32.1, given that journey times and durations are clearly an essential term of the contract and Delay Repay is intended to provide liquidated damages for when the agreed timings are not adhered to.
The Consumer Rights Act 2015 renders 'unfair' terms non-binding. A term is unfair if it causes a significant imbalance in the parties' rights to the consumer's detriment, contrary to the requirement of good faith (see section 62). Schedule 2 of the Act sets out an indicative list of terms that may be regarded as unfair, including:
- Paragraph 11: a term enabling the trader to alter the terms unilaterally without a valid reason specified in the contract. Condition 32.1 does not list any reasons why timings might be altered, nor do timetable amendment notifications give reasons for changes.
- Paragraph 12: a term enabling the trader to alter the characteristics of the product to be provided, without a valid reason. The timings are a key characteristic of what you're paying for but can be arbitrarily amended based on the wording of 32.1
- Paragraph 14: a term giving the trader the discretion to decide the meaning of terms or their application. In this case the industry purports to allow itself to decide what the key terms of the contract are, and what "delay" means.
I wouldn't expect any success if raising a rejected/underpaid claim as an internal complaint or subsequently escalating it to the Ombudsman. Both will likely just look at the wording of the NRCoT, and point out that it says the timetable on the day counts.
Neither are likely to look beyond that and determine whether that's an unfair term, so you would probably need to take legal action to get any further. In turn, unless the value of your ticket and thus the compensation at stake is particularly high, it's probably not going to be worthwhile taking a refusal/underpayment to court.