Influenza A virus populations contain substantial genetic diversity. A major contributor to this diversity is the ubiquitous production of deletion-containing viral genomes (DelVGs) - viral RNAs with large internal deletions. DelVGs directly compete with wild-type (WT) genomes and have been implicated in modulating disease severity. However, the specific functional and genetic interactions between DelVGs and WT genomes remain poorly understood. To examine how DelVGs and WT genomes co-evolve, we serially passage influenza A virus and use next-generation sequencing to build a longitudinal profile of DelVG emergence and dynamics. Highly diverse repertoires of DelVGs observed in early passages undergo sharp contractions in overall diversity, leaving only one or two DelVGs that persist at high frequency. We also identify a recurring substitution that significantly enhances DelVG replication and interference potency. These findings reveal DelVGs to be dynamic genomic elements that are subject to unique selection forces and actively shape viral population dynamics.