Yes, the Espruino bootloader sits in the first 16kB page of flash - so that's probably the first thing that gets removed when you upload your own code - I'd be pretty sure the issue is just with the code you're uploading.
Espruino is a JavaScript interpreter for low-power Microcontrollers. This site is both a support community for Espruino and a place to share what you are working on.
Yes, the Espruino bootloader sits in the first 16kB page of flash - so that's probably the first thing that gets removed when you upload your own code - I'd be pretty sure the issue is just with the code you're uploading.