How to combine 3 chips as one?

[Nicholas_Bokulich]

@ssbbrr

will there be an overlap between samples with the same barcode sequence or not?

In general, no: the barcodes do not matter at this point, since you have already demultiplexed.

HOWEVER:

@ssbbrr

they have the same barcode sequence and sample id, should I change something?

Yes! Change the sample IDs so that all samples have unique IDs. In general, integers make bad sample IDs — use a more readily identifiable or at least unique sample ID. Using an integer ID will not only result in naming conflicts like this, it can also cause some downstream analyses to bug out (and I don't mean just in QIIME 2 — I mean everywhere: if you use R, statistical software, even Excel for downstream analyses)