Steve,
I have put different brands of varnish over the previous coats and had no problem. I have never used Flagship but to be sure you may want to try a sample on some scrap; I just haven't run into a problem switching between most brands of varnish. Before I would sand all your varnish off, I would just keep putting more on as it will give additional UV protection. In other words it may take more coats of one brand to get the same protection as another. the time sanding it off.
As to the last coat that is always a problem when a problem occurrs. If you sand it will leave a sand mark. I have found that if you make the last coat you are going to put on a light coat, you can reduce the sags. The sags are a sign of too much varnish. Also when you are putting it on a vertical versus a horizontal surface, you will get more sags.
Alex warren