How to keep mesh exactly as it was after a simple modifier when I join it up with another object I'm a newbie to blender so sorry if this is a simple question.

I took a cylinder and 2 half spheres joined them and then bridged edge loops. I need something that is thinner in the middle so then I used an add modify / stretch which gave me the form I desired in the middle part, but squished the spherical caps. I removed them and I'm trying to attach new half-spherical surfaces back. The problem is that the moment I join them the stretch is re-applied again and destroys both the spherical cap and the middle part. 

How can I make the modifier not re-apply after join? Thanks.

PS I cant upload a picture for some reason :(
Without an image it's hard to guess which form you exactly want to achieve, but if you would like to make the cylindrical part thinner I would add some loop cuts and shrink them to your liking.