As with anything, it's the execution rather than the number of times it's been done before.
If you write an engaging story, the readers aren't going to think "oh, this has been done so often before". Make it unique, make it interesting, put your own stamp on it (which you'll be doing when you
decide which parts of what myths are "real" in the story's universe) and they won't care.
Do it badly and you can guarantee that one of the criticisms will be "the idea has been done to death". It's only ever "done to death" when the reader doesn't actually like the story. If they like it, it's "a refreshing and innovative approach to the fundamental building blocks..."
As Maddie said, as long as you don't claim that your book is based on facts when it patently isn't, you should be fine.
I've read a number of stories where they've taken different mythologies and melded them - and it can be done very well and make for an interesting story in an intriguing and marvelous universe.
Unless you're making a slavish copy of someone else's All Myths Are (at least partially) True universe, you're going to handle it differently and your story will stand on its own merits.