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1. The theory of the phenomenon applicable to understanding other similar phenomena has long been under suspicion about its accuracy.

2. The advantage of the theory applicable to solving the phenomenon is under suspicion.

Q1) Are both 1 and 2 correct English?

Q2) In sentence 1, what is "applicable" connected to? (I mean what does "applicable" grammatically modify or describe?)

The theory or The phenomenon?

Q3) In sentence 2, what is "applicable" connected to? (I mean what does "applicable" grammatically modify or describe?)

The advantage or the theory?

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fire11. The theory of the phenomenon applicable to understanding other similar phenomena has long been under suspicion about its accuracy.
2. The advantage of the theory applicable to solving the phenomenon is under suspicion.
Q1) Are both 1 and 2 correct English?

These are both poor or confusing sentences. I think it is hardly worth caring about them.

Comments  

For your questions, I see they have been commented but I do have a curious question, where did these questions come from? Apparently, they are not native English, nor they are correct. As suggested, it is not worthy of anyone's time to pursue the meaning or the grammatical correctness.