Unlike a bank, an EMI is required to hold 100% reserves. EMIs cannot lend or engage in fractional reserve banking. Everything is prepaid and funds placed with an EMI are held in separate, ring-fenced accounts (Client Funds accounts) which must not be used for anything other than reserve. Most regulators check these reserve accounts on a monthly, quarterly, or annual basis. Some even check in real-time via API provided by the EMI's financial institutions.
So if an EMI fails, the funds held in the EMI should be fully recoverable by the customers, regardless of the amount. Short of fraud (the EMI stealing money), this should mean EMIs are safer than banks in case of a failure. If the EMI runs︀ away with the money, you have legal recourse to sue the owners and the regulator︁ would be on your side.