It's an issue where there isn't a determinitive or clear-cut answer, I'm afraid.
The NRCoT and most TOCs' Passenger's Charters set out the TOCs' position that Delay Repay is paid against the timetable "published" (though not in any meaningful sense) at 10pm the night before.
I have severe doubts about the enforceability of that exclusion, given that 10pm the night before is so near to the date of travel that it effectively gives no notice whatsoever, as well as the fact that there is no requirement to notify passengers of any changes, and that it gives TOCs complete latitude over the timetable - ostensibly even if they reduce it to one that is essentially useless for commuters, as in your example.
You also have rights under the Passenger Rights and Obligations (PRO) Regulation, which
sets out in Article 17 the right to a minimum level of compensation (25% of the relevant portion of the ticket for a 60-119 min delay, 50% for 120+ mins) in the event of delays. The issue is that the stated provisions only apply to single/return tickets, and for season ticket holders the legislation essentially 'hands the baton back' to the compensation arrangements decided by the TOC:
I don't think that a Delay Repay scheme tilted so heavily in favour of the TOCs (in terms of the ability to unilaterally vary, with effectively no notice, the timetable used as the reference point) can possibly constitute "adequate compensation". Clearly the legislation wouldn't allow a policy of "season tickets are discounted, so you cannot ever get compensation". But the precise latitude afforded to TOCs is something which is legally undecided.
What is more clear-cut legally is the right to re-routeing under
Article 16, which entitles you to re-routeing at the earliest opportunity when a delay of 61+ minutes is anticipated. "Delay" is defined in
Article 3 as meaning:
The TOCs can't insert their own definition of "published" into the legislation (certainly not in a manner that is unfavourable to passengers - see
Article 6). Any by any sensible definition, the "published timetable" is something that is published several weeks or months in advance, not a few days, let alone 10pm the night before.
So as Southern have, presumably, refused to arrange any ticket acceptance to enable you to get to London on alternative routes, they are at least liable to pay for your costs of arranging the re-routeing yourself.
I'm sure you will face some push-back on this. But for Southern to suggest that it's OK to arbitrarily change the timetable in a manner that renders the season ticket completely unusable for its intended purpose, yet for you not to be eligible for any recourse, is clearly insupportable.