When I loose a ball I want to know about it later

You can change the "end result" of the shot to a lost ball or out-of-bounds in the app. If you choose out-of-bounds the line on the map (between the shots) changes to dashes instead of a solid line so you can see the difference. I do that for penalty areas/etc when taking a legitimate drop just so I know at a glance, even though I wasn't technically out of bounds.

The "lost ball" option should probably do the same thing, but it is understandable why it doesn't. If you're playing by the rules of golf you can't just drop a ball where you think you lost it and play on. You'd have to go back to the original location and re-hit. So if you want to play that way the best you can do is the workaround I said.

What about a water hazzard? I haven't had this situation yet, but it may be possible that your ball ends up in a lake and you take relief according to the rules, the app/watch will assume that you are hitting the ball from the position it landed after the previous shot, and this is not correct.

I just end up letting the app count the distance to the drop area.  I haven't found a way in the app to disconnect shots from each other so I can "estimate" where it hit in the water for that shot distance, then start the next shot distance from drop area.  

A really cheezy workaround in the app could be to add a shot from where in the water you landed to the drop area shot and call the club "lost balls".  Then the "lost ball" drop distance isn't messing up the averages on any other clubs. Not sure how well it works, but you can add a shot from as close as you can get to where the ball hit the water.  Manually add the next shot, but "not in current location" go to the drop area, hit, and see how the app accounts for that.  I'd be interested to hear, or may try it myself next round if I remember.