Does anyone know what would happen if I have multiple instances of 2 different versions of the Wire library running? More specifically it would be different versions of TWI under the Wire library. Let me explain a little bit about what I'm trying to do so it makes more sense. I have an I2C part that will only work if I use a repeated start instead of stop then a start bit when switching from MT to MR. I modified the Wire library and corresponding TWI library to have the option of using the repeated start by putting an additional if statement in the ISR in the TWI code. Let's say I renamed the libraries to something other than Wire and TWI and then let's say I have another I2C device on the bus that does not need this functionality and will use the standard Wire library at the same time. Will there be a conflict with running these two libraries at the same time? I know I could change all the names on the function calls but what about the ISR in TWI? Will the code know which ISR is associated with which call? Let me know if I need to explain this better. Thanks. 
Try it out. You probably won't damage anything.