No, installing eWallet on top of itself or upgrading to a new version will not overwrite or delete your data.

When installing an upgrade, you may be asked to convert your eWallet data to a newer format, but all of your existing data will be there.

Note: on a Windows Mobile device, Windows Mobile 5 and newer will force you to un-install the existing version of eWallet. Just make sure you choose to keep your data if asked about it.