What is the question form of this sentence?
The only way to do X is to do Y.
Is it this?
Is the only way to do X to do Y?
I think it's grammatically correct, but it doesn't sound fluent to my ear.
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That is fine. You took the helping verb "is" and moved it to the front of the sentence. That makes it a question now. You "inverted" the order of the subject and verb. That can be used to make a question that calls for yes or no answer. See "Method 1" at the link at the bottom of my answer.
See this page for some helpful information for handling various situations when you want to make statements into questions: