Hello Bea,
When running split libraries twice, make sure that each barcode is matched to its unique sample name. After running split libraries twice, you will have two seqs.fna file in which each Read has a unique sample name appended to the Read ID. Then you can safely concatenate the two files together using the linux 'cat' command.
cat output1/seqs.fna output2/seqs.fna > combined_seqs.fna
Then you can use combined_seqs.fna for downstream analysis and all your samples will be analized together.
Colin