False shallow areas ?!

Why do I get sometimes false shallow areas in open water?...and sometimes not? Also when I import Side imaging data it says "wronge beam buddy" but is doing it anyways!?

How shallow are you talking about here?
Are these present in the original data?
Could they be where the unit has lost the bottom reading for some reason?

Those are zero depth marks,...so far I can only delete complete tracks whit those but the remove all zero depths function does not seem to work (does not do anything).

If I than avoid the tracks with those false readings I still have the maps in my lake master file.
What do i need to remove from my card to start a map completely over?
What files have to be there to restore the original file system on the SD-card?

Thanks

Steffen