Mexican Church Records in other languages!

I just wanted to write about something that caught my attention in the last few weeks. I used to think that Spanish was all that I needed to read Mexican church records. To my surprise, I was browsing some online films from Guachinango, Jalisco, and discovered that at a certain time, in the 1800's, whole parish books were written in Latin! Even the names of the people involved were latinized by the priest who recorded them. This caught me by surprise because I had never encountered this.

I thought, well, Latin sounds somewhat like Spanish, and I guess it won't be impossible to decipher if I ever need to look for an ancestor in one of those parish books. Well, just today, I was doing some indexing for familysearch, and I opened a batch from Mexico City to work on. To my surprise, it was all written in what appears to be a Native language, I assume Nahuatl! I tried to index it, but it was just impossible! I had to return the batch and work on another one. Has anybody encountered similar church records in Nahuatl, Latin or other languages? What do you do in these types of situations if you have a strong feeling your ancestor is in that particular book?