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I am a senior finishing dual degrees in chemistry and mathematics and missed an exam in an upper level chemistry course due to a brief hospitalization which was fully documented. I was granted a make-up exam by the instructor along with a few other students. Our exam was 14 pages long, five pages longer than the original, and incredibly difficult in comparison. Several questions were structured in such a way that knowledge of very obscure and minute details from the 800 plus lecture slides and 200 plus pages of text was required. Without exaggeration, the make-up was perhaps 5 or 6 times harder and significantly longer for the same amount of time. I have no doubt that I failed and will be lucky if my score is even 60%. What actions, if any, should I take? I plan to talk the instructor when my grade posts, but I doubt that is going to get me anywhere. After spending at least 48 hours studying in the last two weeks, this feels very defeating.

Given that exams are difficult to create, especially make-up exams, it is just possible that it will work out when the instructor sees the results. I doubt that it was any sort of 'retaliation'. Wait for the grades and have a conversation.

It is too early to take action until you see the actual results and their effect.

Let me note that for some sorts of exams, writing intelligently about the problem is enough. If the problems are especially difficult then it may not really be possible under exam constraints to find a proper solution. But if what you write is "sensible", and demonstrates that you have the required knowledge, it may be enough, depending on the person interpreting the results. In any case, it is pretty much impossible to treat the results as "equivalent" to those of the normally given exam. A sensible instructor will recognize this.