Which embodiments the underlined preferred embodiments refer to is/are unclear.
Looking at this sentence it might be easy to think that the subject of the verb BE, which heads the predicate is embodiments or perhaps preferred embodiments. However, the sentence has the following structure:
We can see straight away from the sentence above that the Subject of the sentence is the constituent X. In the Original Poster's example, X is an interrogative clause:
- Which embodiments the underlined embodiments refer to
We can see that it's an interrogative clause by making it the compliment of the verb ask:
- She's asking which embodiments the underlined embodiments refer to.
When the Subject of a sentence is a clause, we always see singular verb agreement:
- That she is not here yet is problematic.
- For her to do that is undesirable.
Therefore we need singular verb agreement in the Original Poster's sentence:
- [Which embodiments the underlined preferred embodiments refer to] is unclear.
It does not matter if the Subject of the subordinate interrogative clause is singular or plural.