This refers to territories that start out conquered, I believe.
For instance, if your capitol is lost and your ally liberates a territory (that started the game with a control marker on it) then keep the old control marker there, just place yours on top so that when it is liberated later, it reverts to the correct owner.
For instance, in 1942 Japan begins with Kwangtung. If, let’s pretend, England was under the control of Germany, and then America took Kwangtung, it would now be American. Therefore, you place the American control marker on top of the Japanese one.
Then Germany liberates Kwangtung, they do not gain posession of this territory because it was originally Japanese, so you liberate it. Therefore, remove the American marker and leave the Japanese one to show ownership.
Basically, you’re stacking control markers to remind you who owns what originally.