> You can't have a replication crisis inside of a deductive framework without changing the framework.
You may change the framework, but the replication crisis would be that people don't notice it's changed.
A proof can get so huge and complex that it would take a lifetime of study to understand it. One of the article's good points was that "you can replicate a math paper by reading it", but if you cannot read a proof, you cannot replicate it. If nobody can understand it, nobody can replicate it. There would be a big crisis if people started trusting huge papers blindly and using their results without stating them as assumptions. Mathematicians are largely not doing that, so there isn't really a crisis. But they might! And you would not notice that the framework had become inconsistent for a while. Therein would lie the crisis.
It is nice to think that as soon as the framework changed, people would notice, because surely if it the ground moved, that would be obvious! But it is not true. Nothing about the deductive-ness or in-framework-ness of mathematics changes this. It is the same for psychology, the replication crisis is a crisis because people do not notice these results are wrong, and then rely on them in clinical guidelines and affect people's lives for generations.
It is possible to stave off replication crises by using a machine, because mathematics is self-contained and you can use a computer to show that you proved something using only these specific assumptions and they can believe you without reading and understanding it fully. But this doesn't mean mathematics cannot ever have a replication crisis.
I think your arguments here are best summarised as confusing "replication crisis" with "any published results being inconsistent with previous results". Your idea of "inconsistent" is also strange, the article considers this to mean mistakes in proofs, whereas you mean new mathematics that changes the field by discovery. You're just talking about something completely foreign from the concept of a replication crisis.