If the chunk resetting is related to Enderstorage then I believe it is somehow caused by how stuff like Enderthermic pumps, Quarry+ etc. do chunkloading. Cause I was having constant chunk resets when using a Enderthermic pump+Endertank. Replaced the Enderthermic pump with a normal BC pump + ChickenChunks chunkloader and haven't had any issues for months since. And personally using/have used Entertanks in almost every other possible combination and never had issues with chunk resets in those cases.
So think it is caused somehow by the "dynamic chunkloading" used by Quarry+, Enderthermic pumps, Ender Quarries etc. and it not unloading the chunks properly during crashes/improper shutdowns.