I found that upgrading makes the resonator that was there effectively disappear; It doesn't get dropped, it doesn't go back into your inventory. It is no more.
However you can save yourself some trouble by not pressing the deploy button or swipe action. Select the portal, select upgrade portal, scroll through the empty slots for resonators, and on each slot scroll through your resonator inventory exactly specifying the level you want to put in that slot. No need to upgrade over an existing one unless you're actually looking at a portal you didn't just capture (say someone on your faction put down a bunch of L1 resonators) and want to upgrade.
The shield will be lost when it is removed. You don't get it again.
EDIT: 27/04/15
Added new shield: Axa Shield, and new shielding values
Now the shields have other protection:
- Basic : +30
- Rare: +40
- Very Rare: +60
- Axa Shield: +70
NOW Shields can't be removed
TAKE care with it, if you have the new shields, remove your old shields in your portals, and replace it with the new ones.
This shields.. are...very... helpful for your faction (or not if the portal is of the other faction)
EDIT 2
If you have "old" shields in your possession (this one that have C:+6 R:+8 VR:+10 )
DON'T USE IT! First of all, DROP it, then acquire it again. Why would you do this? That is because, when it is dropped the game recalculate the values of the shields, so the old one convert to the new one.
I mean, if you have a common shield (+10) and you drop it, and acquire it again, the shield will take the new values (+30)
Best Answer
When a portal is moved, it is lost and recreated as new.
All previous links, fields, and mods are lost.