Is it necessary to extract RNA from all samples (replicates) on the same day?

I am working with an RNA binding protein in Ustilago maydis. Deletion of the RBP cause aberrant cell morphology in the organism. I want to perform a differential gene expression analysis between wildtype and the RBP mutant U.maydis strain. a few days back, I sent my RNA samples for sequencing. The design of experiment is, two groups (wildtype vs RBP knock out mutant) and 3 replicates for each group. My problem is out of the 6 samples, The 3rd replicate in both the wild-type and mutant sample was prepared completely on a different day (but the experimental condition was the same!!). I am so worried what if this two sample will cause a major problem in my data analysis??