InDesign Document in Spanish Only Creates English Index

I think that you're going to need to bring in a Spanish translator, or at least have some Spanish knowledge yourself, in order to regenerate a new Spanish index. I'm not sure, though; this post would be one heck of a flowchart, if it was going to guide you through the many possible issues that you might face. However, a few of your questions are easy to answer right off the bat:

The index was previously all in Spanish. [...] I don't understand how they created the index in Spanish from these InDesign files.

When you generate an index (or a table of contents, for that matter), InDesign makes a new story. When you run a typical InDesign document through a typical translation workflow, usually what you do is export an IDML file, which can be consumed by some kind of translation tool or environment, so that the translators are working in a translation-friendly software environment. There's a chance that someone bilingual just opened up the INDD and started translating, or maybe someone copied translated Spanish out of MS Word and pasted it into the INDD, but those are both awkward and inefficient workflows. Usually, dropping the IDML into a tool meant for translation is How Things Are Done. So each story in InDesign winds up being its own XML file inside the IDML.

The upshot of this workflow, for your purposes, is that someone translated the terms in the index, which from the point of view of the translation environment is just another story in an InDesign file. That's how the index in the previous version of the Spanish file was created, I'm guessing; just like any other story in your document. Then, if any page numbers had changed, they were updated by hand, not by generating a new index.

How do I change this so that all terms are in Spanish.

Well, how much Spanish do you know? You're likely to need a Spanish translator to help you finish. I'm not a native speaker of Spanish who makes indices professionally, so if I were in your shoes my first choice would be "I'm going to go find a SME who is a professional Spanish-language indexer." But let's say for the purposes of this thread that you don't have an infinite budget and a mandate from the c-suite to make this translated document the absolute best product that it can possibly be. Then, you'd need some way to update the topic list. 

The way I (as someone halfway competent in Spanish) would approach this would be to search the document for ^I, which is the Find/Change dialog shorthand for "index marker." So I'd find terms marked for index inclusion in the body text. The terms in the body text will be in Spanish, but their corresponding term in the Reference section of the Index pane would be in English, right? I'd copy the indexed term to the clipboard, double-click on the term in the Reference section, which would open up the Topic options, then I'd paste in the translated term. 

There are lots of ways this can go wrong. For example, what if the English topic is "Bread" and there are multiple translated Spanish terms in the document ("la barra" or "el bolillo" for baguettes and rolls, respectively) and you'd need to know those terms (and some Spanish grammar rules, most likely) in order to connect them correctly to the terms in the topic list.  

If I were the localization engineer in a translation agency, and your business was our client, I would know that most or all of the terms in your document were already in my translation memory database (because we did the main body of the document!). So I'd say to you "Just generate your new index with English terms; send me your IDML, and I'll run it through the TM again tonight." Then I'd isolate the index in a separate document and run in through my translation memory database, and you'd get updated page number references and a Spanish-language index. 

Sorry for the long post, but the above is barely scratching the surface of What Might Have Happened and What May Yet Go Wrong.  If it's not enough, post some more details (or, as Anantha suggested, some samples or screenshots) and we'll figure out your least-painful way forward. 

It's not entirely clear what's up here, but nothing in InDesign or pretty much any other standard app would translate or swap words in an index or the like. The index must be using stored English words and terms. I'd hazard a guess that the document was originally English and perhaps translated to Spanish, a process that might have missed the index, but there are problems with that scenario. (A replacement of the text by a translation service, for example, would have deleted or rearranged the index markers.)

@Joel Cherney might have a clue, since I know he does a lot of translation work directly with InDesign files. Not sure there is anything that can be done to fix the problem — if a Spanish index isn't in there, it will be hard to change out the English one — but if anyone knows, it'll be him.

One quick thought, though: have you looked in the Index pane, hamburger (3-line) menu, to see if there is a second, Spanish index? ID allows multiple TOCs, Indexes, CrossRef lists etc. and it may be that you simply have the wrong index enabled.

Hi, 
Could you please share the sample files or screenshot?