I will be completing an engine swap in the near future (Gen3). The car has been sitting for some time ~2 months and the display shows the HV Battery to be drained (last bar on indicator) I did an engine swap on a Gen 2 a few years ago with the HV battery in the same situation. Once I got the replacement engine in, it charged the HV battery but ended up failing shortly there after (~3weeks)... coincidence or result of it being drained and not in use? How does a drained HV pack that is not in use affect its health, if at all?
The term "fail" needs further clarification. It is usually not the entire battery that fails, but 1 or 2 modules that lose their charge more quickly than the others and, if no corrective measures are taken, will become more and more out of balance with each charge / discharge cycle. In your situation, I believe it is essential to know the condition of each module before you put the battery back into service. Dr. Prius or Techstream would be able to give you an indication of which modules may be problematic. If you are capable of swapping an engine, checking and, if necessary, refurbishing any modules that need it would be within your abilities.
Seems Old HV packs start to show their age / fail soon as there's a change in vehicle routine... Whereas cabs in a big city that almost never stop driving can go 1/2 million miles without a pack issue. Because you've done more than one engine swap I think you'd benefit from this thread we started yesterday: Build Hybrid Battery Maintenance Gear For Under $100 | PriusChat