With just one bar on the battery meter the battery must be close to being fully discharged and when that bar begins flashing it is saying it is about to switch off as there is insufficient current available to continue. My phone does the same thing - except as my phone is powered by a lithium battery, when it is dead it stays dead.
Your scooter probably has a lead acid battery, an old imperfect technology that accepts charge slowly and discharges the same way - when seeming to be fully discharged while under load when switched off for a brief while they tend to recover slightly, especially if the battery has one cell that is faulty..