Issue with Cloudflare after website restore

I am using Cloudflare and its APO feature. Today I restored my website from the previous back up but after restore my website was not opening properly. (some directory structure was shown)

So my hosting provider changed DNS to point directly to the hosting server instead of using Cloudflare DNS. After that website started opening properly.

Is the APO feature caused this issue?
I want to know how I can restore my website while using Cloudflare next time without causing such issues.

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