I'm certainly not an expert, having only had V5 for 3 weeks, but it looks to me like upgrading to V6 just overwrote the existing *.dll and *.exe files from V5.
For example, after upgrading to V6, I only have one copy of "ARP 2600 V3.exe" and two copies of "ARP 2600 V3.dll" (one 32-bit, and one 64-bit) on my hard drive.
I don't know if perhaps there are other files between V5 and V6 that are duplicated somewhere else on the hard drive.