Hi @azan, welcome to :qiime2:!,
For the case in which you have data from amplicon region, but with different primer pairs, there are a few options you can try below. Note: regardless of the approach you use, you'll still have to worry about slight variations in PCR / sequencing biases in your results. Which may inflate differences between data sets. It only takes a single base in a primer to alter what you observe in your data.
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Alter the trim & truncation settings for each run, using these slightly different primers, such that the the same ASVs will be generated. Then you can merge the tables and sequence files for down stream processing.
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Closed reference OTU picking is another option. I suggest you read He et. al. 2015, Rideout et. al. 2014, Wescot et. al. 2015, and finally Callahan et. al. 2017 for more information.
EDIT: Do not use approach 3 below for combining multiple data sets. I erred in my thinking. See later post.
3) You can use q2-sidle, to treat these as different amplified regions to combine your data for each primer set.
Just as an FYI, I am also currently combining data sets with different V3V4 primer sets. In my case, only the reverse primer is different between the two. Thus, I am currently using the 1st approach I mentioned above, as I only have to trim a few bases of the end of one of the sequencing runs.
Anyway, that's my two cents. 
-Mike