English has some restrictions on word order and has rules about the order and position adverbs occur in. (The ordering is based on the meaning of the adverbs.)
Moving words out of the expected order, termed anastrophe, can give information about the intended meaning, but unfortunately this was not done.
The sentence could have been written as
Today he found the bicycle that he had lost yesterday.
If so it would mean that finding occurred today and that losing occurred yesterday. (Note it would not have the same meaning as the original sentence in this case!)
This change clarifies the meaning of yesterday because it forces us to think of yesterday as part of the bound relative clause.
However we cannot know for certain what the writer means because they didn’t include that information.
In summary yesterday could be either inside or outside of the relative clause that he had lost.
If inside then yesterday helps describe the bicycle. Outside it describes the act of finding the bicycle.