Pulling a case out on the 550b to check the primer depth is easier to do than it is on the SDB. Priming on the 550b is done in the first position and the SDB is the second position. On the SDB you have to pull the positioning pin to remove the case to check it. Having the press set to the right height makes the operation easier too. When I press in the handle to set the primer on either one I can feel it start to go in and can pretty much feel it bottom out. When I'm not quite certain if it seated fully I will press the handle in again before going further. I have yet to not fully seat a primer on the SDB press. I did have a few problems on the 550b in the beginning. I got the SDB after already loading a lot of ammo on the 550b. I probably had so few problems with the SDB because of my prior experience with the other press.
Now that you know this can be a problem I'm fairly certain you will have it happen a lot less in the future. The Dillon guy seems to have the best solution for you. I didn't think things through enough and should have suggested pulling the bullets prior to trying to finish seating the primers. Doing short cuts when you first start out is probably one of the worst things to do.
When I make my second test of a load I have worked up I normally only load 50 rounds to see how it does for a longer test and to check how well it burns. I prefer a cleaner burn if I can get it and stay accurate. Once that is checked out I tend to load several hundred for a full range trip test. Normally by that time I have pretty well made up my mind about the load. I still have several hundred rounds loaded of some ammo I loaded a while back while trying to find alternate loads I could easily use if I couldn't get the powder I prefer to use. I found some combinations that worked better than what I started with. You just never know. I guess one day I will have to shoot those too just to have the cases available for the better load. At least now if I can't find the powder I really like I have some others I can easily switch over to until the other one become available again. This comes in handy when supplies are short like now.