Here is a little trick IF you have spent primers that have backed out of the case and you can no longer fit in the SH.
Extend the decap rod a ways out of the bottom of the die
Put the case ON TOP of the shell holder.. centering with your fingers as the rod enters the neck.
Just push out the primer without letting the case enter the die deep enough to size. It helps if the decap rod in longer.
But it doesn't resolve the concern you have... First off, review the loads you have used to see if overpressure might be a possibility. If these were factory ammo, see if you can match lot numbers of the ammo to brass that no longer fit.
Have to assume that ALL brass in question fit the SH before firing????
Of the cases that will no longer enter the SH, make sure the primer is indeed flush with the bottom of the case so you are measuring the extractor groove with the SH. If the case doesn't enter AND the loads are within printed specs and velocities agree, you likely have brass with soft case heads.
If you have an oversized chamber, you can swell the case heads with normal pressure loads so you have to check all options before concluding it is a case issue.
Make sure the bolt locks up properly and headspace is within spec. With this chambering, assume this is a custom rifle?
Can you get out of spec brass, of course... every manf has had an oops now and then.
But make sure it isn't elsewhere in the rifle.
Jerry