let say you have a 18" rims you lowered it then need some fender rolling, spacer etc etc...
then afterwards you decade to change the rims to 16" stock rims.
is there any issue if you downgraded from 18-16?
pretty sure its gonna be more lower right? by 2" am guessing here.
is there any other issue? anyone?

 

it doesnt depend on the wheel so much as the size of tire. going back to 16's is fine, but make sure you get the right sized tire. go off of oem tire size as the oem wheels are 16's

wheels specs will come into play as well, like width and offset.

 

you don't have enough information to answer your question. There is more to fitment than just the rim size, you need offset and size of the tires. you can have the exact same wheel profile on a 20 inch rim as you do with a 14 inch rim if the size of the rubber makes up the difference in the side wall.
just a quick reference, 195/60/15 is the same profile (height) as 225/35/18.

Here is a good calculator for comparing sizes. Other issues with fitment is to do with the offset of the wheel. Do some more reading or go to a tire shop and ask them for help to compare.
I have a couple different wheels that I run.
195/65/15 on stock rims 15x 6.5 38 offset
185/50/15 on XXR 513 15x7 15 offset
215/35/18 on GIO 732 18x7.5 38 offset

I am lowered on DF210s and have no rubbing issues on any of these tires.

Here is a good website to help with see if the setups are close to what you need.
http://www.rimsntires.com/specs.jsp

 

what they said. plus, if there is an overall height difference of two inches (height of tire i mean) then it would only lower it one inch, because that would be one inch above and one inch below.

 

you're probably lower than i am, but i just took off 18x8s w/225/40 tires and put on 16x7s w/215/55 tires and it's all the same.