Sequences with identical descriptions but different lengths are likely orthologs from different species.
You can filter them by sequence identity using CD-HIT. If you select a 90% identity cutoff, it will cluster together all the sequences that share 90+% identity, and keep a single (and longest) sequence from that cluster. That will likely take care of your partial sequences without having to grep them out.
It is up to you to select whatever identity threshold makes most sense. More sequences will be retained at higher cutoffs.