I honestly think it was just a plot hole. The reality is that Fairy godmother had a deal with Harold. One that if he broke, his happily every after (his human form) would be taken back as well. Not to mention, they were still the rightful rulers.
And with the time frame as it was when this was happening., Charming was already on his way to save Fiona. He was just a tad bit late. I’d say a couple months late if not less as when he got there, Fiona was on her honeymoon.
Some people might say that he would have heard about the change in leadership before he saved her. But no not necessarily; Fiona had her whole identity and inner beauty shtick journey, got married to Shrek, went on her honeymoon and traveled to Far far away and Charming didn’t know ANYTHING about it. Not until he literally arrives at the castle and there’s a wolf in the bed who tells him she’s on her honeymoon last he heard.
So if Shrek never saved her and they did sign away, Charming should have gotten to Fiona and rescued her. Charming may be stupid but once he learns something is wrong, he most likely would have fought for what he believed was his right to the kingdom. And as we saw...he’s more than capable of organizing a successful take over. And this time he would have his mother full magical arsenal at his back. And fairy godmothers magic is STRONGER than rumplestiltskinsRumpelstiltskin's as he was unable to reverse Fionas curse, something that Fairy Godmother could do and was her doing in the first place. So Unless the Fairy Godmother turned her eyes somewhere else after Harold's death or Rumpelstiltskin got a different deal with her.
So in short. Charming should have absolutely rescued Fiona. But again they stretched themselves too thin and did this movie as a money grab. So... there’s a huge plot hole.