How should I address batch effects in my experiment?
Yes, though thankfully Your 2018 PreD samples will help you resolve this.
Simply add the batch effect to the design (~Batch + Treatment) and DESeq2 (or edgeR or Limma) will handle this for you.


You do not need SVA or RUV, thankfully, since you quite cleverly sequenced one group in both batches.

To clarify, your coldata will be something like:

Group    Time    Batch
A        Pre     A
A        Pre     A
A        Pre     A
A        Post    B
A        Post    B
A        Post    B
...
D        Pre     A
D        Pre     A
D        Pre     A
D        Pre     B
D        Pre     B
D        Pre     B


And the design is actually ~Batch + Group + Time. You can probably add an interaction term in if you then modify the model matrix manually to ensure it's full rank.