[BioC] batch effect confounded with condition

[tefina]

Dear List,

I have microrarray data where condition is completely confounded with a time
batch effect. When doing a PCA on the RMA normalized data, the first principal
component separates clearly the two batches.

What option do I have when I still want to compare different conditions across
batches?
As far as I understood I can't dissolve this batch effect neither with limma nor
with e.g. ComBat.
Shall I just go on with the limma analysis and keep in mind that some genes just
might pop up due to batch effects?

best,
tefina