Sure you can. You just have some code like in WalletAppKit that does the following:
boolean chainFileExisted = chainFile.exists();
boolean shouldReplayWallet = vWalletFile.exists() && !chainFileExists;
BlockStore store = new SPVBlockStore(params, chainFile);
... later ....
if (shouldReplayWallet)
wallet.clearTransactions(0);
Now when you start things up the wallet will contain only keys (and, uh, extension data, but that's a bug). The chain file will start at zero or wherever you checkpointed to (i.e. earliest key time), the wallet will have no transactions in it, and the replay will get you back in sync with the network.