you should be able to do that just fine as long as you make sure you have a "hard" save (manual save not done by auto or quick save) prior to activating the mods and those mods are removed before attempting to use this pre newly added mods save
just be sure you keep things situated and you can always return to your starting point. (dont trust your memmory, create a text file and write down your mod list, install order, and new mods added and there install order)
but a word of caution, some mods will only work if installed while you are in port, in these cases it is usually clearly stated so read the install info.
as a rule, when doing what you are talking about, just for peace of mind that things will work trouble free, i would return to port before doing it reguardless of any mod instructions that it may not be required.
better safe then
trying to find why some mod feature isnt working