I had the same question a few years back, so I called National Refrigerants to get a difinitive answer. They said that the HP blends, 402a 404a 408a and so on have a much lower chance of fractionating, so if you can get the majority of it out, you shouldn't experience notable capacity loss. On the converse, the MP blends, 401a 401b and so on, fractionate much easier and a lot of forethought should be used before reusing this gas. I would, if possible, get an oiless liquid capable recovery machine. This would allow you to get the vast majority out in the liquid form and a lot faster. If you have gas recovery only, make sure you have POE oil in recovery motor compressor and get all of the charge out.
My general attitude about 404a has been to go back with new stuff in all ice machines and reach in equipment. Even on walk ins that I know have less than a full bottle, I will put new gas in. However, with the above stated, on larger systems,I would reuse clean gas on the equipment it was removed from if I got the overwhelming majority out of it.