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Are those IPSs of the same ROM?
If they are then yes, changes will be applied if you apply the newer to the older.
If they are different, you risk encountering bugs.
Depending on which IPS's you add first can make a difference. But yeah, bugs can happen and the game may crash at a certain part, or even the game may not load. Why do you need to add 2 IPS's to the same rom by the way?
Because I was thinking if I could do a team to make a hack, each one with a different function. So, they make a IPS file, send to me, I apply all and put the "complete" to download. Sorry for any grammatical error.