I'll go through your question clause by clause:
I've made an offline address
You're doing good.
and only have the key stored on 2 encrypted flash drives stored in different locations
As long as only you know the password and the password is sufficiently strong, this is probably secure.
with the private key written physically on paper and stored in 2 locations.
If either of these two locations are accessible by anyone other than you, then they are vulnerable. If someone else found either paper, and your keys are in plain text, then you could consider them compromised.
Do I ever have to worry about my coins?
Yes.
That is, could they ever be lost in software changes
Extremely unlikely, as the whole of Bitcoin depends on the safety of balances through upgrades. There are people who have very vested in ensuring that this never happens. Even a bug in the protocol could not erase history in an unrecoverable way, as a single offline client copied online or bootstrap.dat would refresh anyone affected.
or is that as big of a never-going-to-happen as the 21 million limit being lifted?
Pretty much.
I'm pretty sure I'm not touching that wallet for a long time. Is there any benefit to repeating this process for a more "fresh" address ever or does that not make sense?
Theoretically, you would never need to regenerate keys unless some kind of vulnerability was found in the software that generated your key, ala the Android random number generator flaw.
An unlikely occurrence would be some kind of change to the way private keys are imported, and your private key generated in 2013 cannot be securely converted to whatever format is expected in 2063, or whenever. I wouldn't get too paranoid about this.
Your answer misses the point here: Since he created his key offline there is no risk that the funds could be accessed through hacking/scam since they are literally not accessible from his day-to-day computing equipment. – Murch – 2013-10-18T12:01:42.820
Hey boss, my assumption is that he will still be conducting some trading and activities online. Correct me if I am wrong, but he will have to reload the bitcoins no? Also, if he used a flash drive, then he used his fingers to type, and there are spyware programs out there that can and will read what you type. – BTC_Hamster – 2013-10-18T15:40:31.277
The asker wrote "I'm pretty sure I'm not touching that wallet for a long time." as in, he will not be conducting trades and activities with this particular wallet. Of course some point in the far future he will re-import his private key to access his funds, but before then, the situation is such as he described in detail: He keeps his private key offline in two different usb sticks and two paper copies. While these types of storage pose their own security risks, they definitely cannot be attacked by hacking or scam. – Murch – 2013-10-18T16:15:50.507
Also he wrote that he created the wallet offline: If he went about that in a sensible manner, he did that as follows or similarly: He disconnected his machine from the internet, booted it with a clean live cd, created and backed-up a new wallet, then shut down the computer again. That way only a hardware spy-tool that stores information through shut-downs could have sniffed out anything, which I find implausible. – Murch – 2013-10-18T16:25:26.220