Hi @t.gousdovas,
Apologies for not being more specific - you would need to add in the appropriate sample IDs in your concatenated file. So for each file, you'd include the sample ID as a new column which would then be included in the resultant file that includes all of your samples. Here is an old forum post that discusses a similar situation, which you may find useful.
Alternatively, if your sequencing provider gave you associated quality scores for your data, they could be converted to FASTQ format, which would be much easier to deal with when importing (as QIIME 2 does support importing multiple FASTQ files into a single artifact). Here is another forum post that discusses this, which you may also find useful.
Hope this helps!
Cheers 