Hey @MajdaD,
Ideally you would import them unjoined, and allow DADA2 to do QC on both directions before merging. This thread has some good discussion on why you'd be better off doing that.
If that isn't possible, you could probably treat them as single-end so long as your read-joiner produces "good" quality scores for the overlapped region between R1 and R2 (see linked thread for discussion), you could use denoise-single.
If that also isn't the case, deblur should work fine on your merged reads, as it works in a different way.