You have to make sure all the necessary information is in ONE file. For example all the changes to CareerStart.upc for each ship have to be included in one CareerStart.upc.
To make it simple to understand an example: TBear is working on a MOD for the Takao, he obviously is not going to add a CareerStart for the King George V. So that means the LAST Careerstart.upc is the only one that will work right.
One progam I have found to be very helpful, especially with Menu1024_768.ini but will work with any file that you edit with notepad is called Winmerge.
So you get the warning for the Careerstart.upc. You open Winmerge and on one side you open the King George CareerStart.upc, and on the other side you open the Other CareerStart.upc (whatever that might be) and it will highlight the lines that are different. That may help you to fix them.
You only have to know what information must be changed and what does not. Another example: If in the Flotillas.upc the missions are different, it is ok to leave one or the other in as long as they are both missions for surface ships.
I don't have the King George so I will show an example of a CareerStart from the German uboat add on that we used for TBear to test the ships before he got his 'campaign' going.
As you see on the left is the Careerstart for the Takao and on the right is the Careerstart for the Furutaka. And the difference is highlighted. So obviously for it to work both ships have to be in one file, since as you said the last one installed overwrites the old one.
So this program may help you it may not. But it will show the difference in the two files.