OP's concern is valid. What if your old wallet format does not get recognized by new clients and the old clients are not able to send transactions after 2 years? (private key is relatively safe but still... see below)
Install an older client and dump your keys. Or use wallet management software compatible with the older format
However, if the protocol change is coming from a malicious actor or sybil attack, then old coins might still get lost in a compromised environment
Wouldn't such a change be instantly discarded by the majority?
So how can you store Bitcoins as long-term savings or investments?
Some prefer to store them on encrypted backups stored offline. Others prefer paper wallets. Others prefer a mix of paper and digital... Many secure ways to store them. Obviously one has to pay attention to Bitcoin, in the remote case of what teukon wrote about happens
