Moving a USB from an online wallet to an offline wallet back to an offline wallet defeats the purpose of cold storage was my thinking.
Both plugging in a USB and importing a private key have their own risks. You can't eliminate risk in life, you can reduce risk and limit it.
If a private key and public key are paired they should not effect other private and public keys.
That is generally true, and is certainly true if proper methods are used for generating the private keys.
Obviously the bitcoin client uses accounts to mean something other than private keys
Correct. Accounts have nothing to do with private keys.
which to me makes no sense and makes me question if somehow the private keys are intermingled.
Intermingled? Not sure what you mean by that. They are all stored in the same file, so yes they are intermingled.
Yes if I manually write down a private key from the offline wallet and import it to an online electrum client I am risking the bitcoins attached to that private key but it should be the safest way to not risk the rest of the bitcoins which are connected to other private keys.
Yes, bitcoins connected to other private keys should be unaffected. The main concern is whether or not you are correct about how many bitcoins the wallet actually had associated with the key you imported. If you were using "accounts" to determine this, then you may have imported a private key that had more bitcoins associated than you thought. Therefore, when you thought you "fully emptied whichever private key you imported" there is a possibility that you made a mistake and lost some bitcoins that you didn't account for. It's unlikely, but possible.
I will check the offline client again but for safety reasons it is not easy for me to access.
Good luck. I hope you get it all figured out. Let me know if there's anything more I can do to help.