RNA-seq data with retired transcripts

Question

[dchen71]

So I am looking through RNA-seq data processed via Kallisto/Sleuth and annotated with BioMart and found some transcripts are linked to retired/archived versions of genes. I have also found the regular transcripts which directly map back to current ensembl genes.

For instance, for Flt3l, I get ENSMUST00000150673 for the retired transcript and ENSMUST00000146760 for the one that maps to Flt3l.

As they both have count data, what should I do with the transcripts which are not current?