Is it ok to ChIP-Seq two samples when the ChIP worked better in one?

[biznatch]

We want to do ChIP-Seq for RNA PolII between Control and Treatment (plus input). In the past we've done ChIP-qPCR and it's worked well. To make sure the ChIP worked equally well between Control and Treatment we look at several sites that we don't expect to be changed between Control and Treatment (eg. Bactin promoter, Gapdh promoter, and a few other sites). Usually enrichment is the same at these sites.

Now we have a new sample to send for sequencing but it has higher enrichment at these control sites in the Treatment sample, about 30-40% higher. To me this suggests that the ChIP in the Treatment sample just worked better this time for some reason. If we send send these new samples for sequencing will we get accurate results? Maybe we would get 30-40% more sequences from the Treatment sample but then we would scale the enrichment down to compensate, so the data would reflect equal number of reads between the samples. Usually we have a slightly different number of reads between samples and have to scale the data a bit anyways.

We don't get these samples very often so we'd rather not wait for more if this current one will be ok.