Installed a BN220 GPS unit the other day. Works fine but there is one issue I am having when I change the drones battery. That is I loose all the satellites and have to wait up to five minutes between every battery change for the GPS to find more satellites. 

Has anyone else had this issue?   I noticed a small watch type battery on the GPS and was under the impression this would supply power to the GPS to retain all the satellites in its memory, thats the only purpose I can see for the battery to be there. So maybe this battery has been discharged? Are I on the right track here?

This is normal until that little backup cell takes a charge. I have three of those GPS units and two of them act the same way you describe until they have been powered for about 20 minutes. You can always supply 5vdc from an external source to the unit and let it charge that way. The plug in USB chargers supply 5vdc, you could mock up a cable with just POS and NEG and let it charge for a bit.

In the end, those little units work, but after a year of having to fiddle with them to keep them working correctly I replaced them with the Matek GPS units and those always work without issue.

This seems to be hit or miss for people.  One of the guys I fly with has the same problem you describe.  Me on the other hand have never had a problem.  After the initial connection, follow up connections are quick, usually less than 30 seconds.  I just flew a week or so ago and the quad I flew hadn't been flown since mid September.  The GPS had acquired around 10 sats by the time I could walk from the quad after battery hook up and got my goggles on, about 30-40 seconds.  All 4 of my GPS are the same brand, and all work fine.

This is the GPS I'm talking about, HERE.

I wonder if maybe some of those little units made it out for sale with failed aux power (that little cell that allows for "warm starts").

The one on The Japalura is slooooooow. The one on the 5" is fast like you are are describing. Both are were installed within a week of one another. If I swap the units, the issue shows follows. It is definitely the units, but no rhyme or reason for it.

waynepatt58, you might contact the vendor and ask if they will replace the unit as the one you have is faulty?

I agree with Kaity, try to get a replacement.

thanks for all the comments, I will try to charge the cell up to see if it corrects the problem.