How can I get my cream pie to set?
There are thickening agents you can use without reheating. They won't give you the texture you expect from a starch-thickened pie, but you will be able to cut it. Gelatine is probably your best bet. Others, like xanthan, will make it gooey, but it will still flow a little after being cut. 

By the way, having flakes in it is not a problem for cooking it again. If you mean that you put them on top, you can just stir them in for the reheating. Won't look that good, but will be firm. 

When making cream pie filling, always do it on the stove and make sure that you really brought it to a boil. Egg yolks contain an enzyme which liquidifies starch. The enzyme is deactivated at above 90°C. If you don't heat a mixture with eggs and starch (and flour) enough, it will turn into a soup after a day.