Conventional wisdom is No, you can't mod a can. BATFE considers suppressor "parts" to be suppressors in and of themselves.
So you could probably take out a baffle safely, as that part is already part of the can you have, and is registered. Wipes, specifically, have been considered parts that need registration, so you could not make a wipe and install it without doing a form 1 and paying the tax on the wipe. There is some evidence that you can make a NEW wipe for a can that already had one as long as you don't make spares. You can repair your registered can, but you can't have a pile of spare parts lying around. This counts for baffles too for those of us with lathes.
For example, I have a Form 1 JK Armament modular can. When I registered it, I gave them the OAL with all the baffles installed, and drilled all the baffles at once. Now they are all registered and I can run the can in "short mode" all I want. If I had done the opposite, and registered it with a short OAL and drilled out the baffles to make it longer and had them lying on my bench, those baffles themselves would be an unregistered suppressor.
There IS a case challenging them on this floating out there, but I don't know it's current status. There's also the question of: If you have the ATF pawing through your workshop looking for unregistered wipes, you got bigger issues.