1) Yes you will have to manually navigate if you have lost the navigational path after closing.
2) You can go to the Config (wrench ) Tab. Open Logging and then Sample ID. Uncheck the option for Check for Unique ID's or also can check the option to Renumber Target Sample IDs when a point is deleted. Maybe these options may help your issue. I do, however, suspect that maybe we have logged 2 points on top of each other with 2 different Sample ID numbers, so that could be why it will not allow you reuse the number again.