That is not intended behaviour. What are you playing on? I have encountered a bug in Vice on Mac where EasyFlash saves are lost occasionally. But it appears to be a bug with Vice itself.
Thanks. Could be that the bug is in Windows Vice as well. One thing to check, in Settings > Cartridges > EasyFlash, make sure you have “Optimize image when saving” turned off.
And are you using v1.02?
It could also be a bug with the game, but the only thing that would leave you with no progress would be if it happened after 256 saves when it erases the sector. Did you see if the border flashed before during a save before you lost progress? The flash happens when the sector is being erased.