Qiime produces an error message if the id/header is a duplicate when importing a FASTA. It currently looks up to the first white space (from what I can tell). This should be changed to compare the entire length of the header to allow for sequences from one accession over different ranges. The white space formatting after the accession is important for feeding to NCBI via RESCRIPt.
Here is an example of a format pulled for FunGene which fails to import:
‘>JNFD01000014 location=90164…91795,organism=Sphingopyxis sp. LC81’
‘>JNFD01000014 location=00001…00350,organism=Sphingopyxis sp. LC81’
Edit it add: maybe a flag is ideal to prevent unintentional uploading of duplicates accessions?