לזכות אלחנן בן הענא מרים שיזכה ללמוד וללמד מתוך הרחבת הדעת ושפע רוחני וגשמי
Can Eliyahu decide whether tefillin are kosher if written on the flesh of a fish?
The gemara in Shabbos  asks if one may write tefillin on the skin of a fish. The gemara answers that Eliyahu Hanavi will came and tell us. The gemara asks what this means? Explains Rashi that heter and issur are not dependent on the opinion of Eliyahu because of the rule לא בשמים היא.
The Maharatz Chayus asks according to Rashi's understanding how the gemara often says תיקו which is an acronym for ת"שבי י"תרץ ק"ושיות ו"בעיות. So the gemara itself says in many instances that it is Eliyahu who will decide this question.
The answer is that Chazal have the status of the Beis Din Hagadol [see R' Elchonon Kuntres Divrei Sofrim #4] and they determined that in instances where we have no הכרעה [clear halachic decision], we may follow the dictates of Shomayim. However this does not always apply and sometimes Chazal did not say that we are bound by the decisions rendered from Shomayim. Therefore, regarding the issue of writing tefillin on the flesh of a fish where we have no basis to assume that we must follow the Heavenly dictates, the gemara asked how Eliyahu can rule this question.
So now we have pshat in the gemara in Shabbos. B"H!!!
When R' Evyatar met Eliyahu why didn't he ask him to resolve all of the times it says Teiku?
We see from the gemara in Gittin [6b] that Eliyahu used to appear to Rav Evyatar. The Birkei Yosef asks in the name of Rav Betzalel Ashkenazi why Rav Evyatar didn't take advantage of these oportunuites to ask Eliyahu to resolve all of the s'תיקו in Shas. He answered that there were two different Eliyahus... The gemara in Menachos [45b] says about a certain puzzling pasuk that Eliyahu will expound it in the future. How can Eliyahu rule if לא בשמים היא? He answers in the name of the Rashba that Eliyahu has the power to explain and interpret dinim. But what about the gemara in Shabbos [the fish skin] where the din is not allowed to be interpreted by Eliyahu?? Answered the Birkei Yosef that Eliyahu may decide the halacha based on his intellect and logic and not on any Divine inspiration [see also Ri"z Halevi on Parshas Pinchas who explains that Eliyahu was part of the chain of transmission of the Torah that the Rambam listed and he therefore has the right to decide halachic questions]. But if that is correct then how come the gemara in Shabbos [according to Rashi] wonders how Eliyahu is ruling on the fish skin question? Let us say that he is ruling based on logic and not prophecy?? See what he answers.....
Chazal can tell us to follow Eliyahu
But we can explain as follows: Rav Betzalel Ashkenazi was asking why R' Evyatar didn't ask Eliyahu to resolve all of the Teiku's in Shas. As we explained, Chazal [as Beis Din Hagadol] gave him this right and ability. The Rashba [Menachos 45] is referring to the gemara that says מקרא זה עתיד אליהו לדורשו - so Chazal gave him their stamp of approval and he had the right to interpret that specific din. However the gemara about the fish skins is talking about a case where Eliyahu was NOT given the right to decide, so the gemara correctly asks why it matters what he rules when we know that לא בשמים היא.
R' Chiya chose to follow Eliyahu
In Chullin [36a] R' Chiya is in doubt whether we say ישנה לשחיטה מתחילה ועד סוף - if the shchita process is considered continual from beginning to end [or only starts at the end]. The gemara says that the question is in limbo "לעולם" which Rashi understands to mean that Eliyahu will decide. The Maharatz Chayus asks on Rashi from the gemara about the fish skins where we see that Eliyahu may not decide halachic questions. So how can Eliyahu decide this question???
The answer is as we said earlier that the psak and הכרעה of Eliyahu is not binding but if it does not conflict with any of our rules of psak [such as rov] we have the right to follow him. R' Chiya chose to follow Eliyahu's psak in the future. The gemara in Shabbos is talking about Mar the son of Ravina who DIDN'T choose to follow Eliayhu's psak. If so, why is it binding?! That is the gemara's question.