With the cynics here
Including Dr. Syntax.
DEFRA couldn't even manage to build an IT system to distribute EU subsidies to farmers and kept incurring fines for incompetence.
Designs were not optimal - for instance assuming that all rural farmers had the same kind of fast Internet access available to the developers.
If your current systems are red flagged, what are the chances of using the same resources to produce a speculative blue sky system against unknown rules? You are more likely to ease off on the current systems because they are unlikely to be fit for purpose post Brexit anyway.
I am pretty sure that DEFRA are not alone here. Standard project management to keep quiet about your problems and hope some other part of the project is going to force a slippage and get blamed. Then agree to align your project with the new longer timescales.
Personally, I suspect that the "hard" in hard Brexit reflects the times most IT systems will find themselves in. Will this be a licence to print money like Y2K? Or just an opportunity to build trade deals with non-EU service suppliers which include free movement in and out of the UK?