Question about model design in for RNA-seq experiment

This looks like:

  Sample          Condition
  Condition1_rep1 ConditionA
  Condition1_rep2 ConditionA
  Condition1_rep3 ConditionA
  Condition1_rep4 ConditionA
  Condition1_rep5 ConditionA
  Condition2_rep1 ConditionB
  Condition2_rep2 ConditionB
  Condition2_rep3 ConditionB
  Condition2_rep4 ConditionB
  Condition2_rep5 ConditionB

If so, the design is ~ Condition and the above table would be what DESeq2 accepts as colData. This is sufficient to indicate the samples that belong to one group. Group membership is not indicated via the design formula as you did with pairs. If you want to include batch then add this as an additional column and use ~ batch + condition. Check by PCA first if you see signs of batch effect. If not leave it out. I hope you did not extract all of ConditionA on day1 and B on days?