What effect does removing previously-dried peppers from a sauce have?
Chilis supply 2 things, chili flavor and heat. The flavor comes from the flesh while the heat comes from the seeds and especially the membrane that connects the seeds to the flesh. Ordinarily when someone wants to reduce the heat of a pepper I would suggest cutting it open and removing the seeds and membrane, however that's pretty much impossible with a dried pepper.  

My recommendation in this case would be to put the chipotles in whole, then remove them after cooking is done. Put the peppers in after all the other ingredients, just before simmering, then try to avoid stirring it if you can avoid it - be gentle so you don't burst the peppers open. Once the cooking is done you fish them out with a spoon and you can serve them as a side to the heat lovers if you like.