RNAseq DE comparison with samples of different read length
You don't need to do anything, this is taken care of by the linear model - if you don't have any confounding effects.
If you do have confounding effects, e.g. all control samples on HiSeq and all treated on NovaSeq there's not a lot you can do anyway, other than be honest when you present your results.
Taken care of by the model means adding an extra 2 level factor for sequencer by sample, you need to do this anyway to take care of the batch effect between sequencer runs.