By interleaved I mean that cases and controls were not each in their own run batches, but ideally run A ,B, A, B, Yes ComBat can some of the batch effect if sa

By interleaved I mean that cases and controls were not each in their own run batches, but ideally run A ,B, A, B, Yes ComBat can some of the batch effect if sample sizes are large enough. But here as you point out they are on thin ice.