the classifying liners can help to segregate grinding media inside the mill but is it auto or semi autogeneous mill either these liners work ? pl check with suppliers.
A major cause is the broken and deformed shape grinding media.
Other cause is the filling level of the ground product.

Over filling of fresh feed, an increased recirculating load or an unstable automatic loop that would cause high and low rates of feed?

The cylpebs are not broken or deformed.

We were instructed to put blinder plates on 50% of the discharge diaphragm. We saw the segregation and migration of the grinding media prior to this instruction.

Currently, we have seen a reduction in production in this mill, we have seen an increase in the recirculating load and we are seeing a decrease in the separator efficiencies.

Is the only way to correct the charge in the mill to drop the charge and replace with a new charge?

Closing the diaphragm slots will increase the fineness (finer grinding). This means that the classifier speed should be adjusted accordingly. I don't know what your grinding and what type of classifier and cut size you are running. More information would help.
Do you have a scats removal magnet installed for your mill? Additionally, have you noticed high wear of your cyclones?

We have magnets on both the discharge and the feed end of the mills. Yes, we have seen high wear on the classifiers, not necessarily the blades on the rotor, but the top and bottom plates wear quickly.
We are grinding a Metakaolin, and we use an Ecutec Alpha Classifiers. We have three in parallel in the closed loop circuit. We feed the mill at 24 tph, and we are grinding to a d90 of 14 micron.