Problems compiling ESP8266 - missing "eagle.app.flash.bin"

have you tried a make clean and then a make?

What env have you set up - this is my build script:

root@OFFICE-PC:/mnt/c/ubuntu/Espruino# cat build-esp-4mb.sh
#! /bin/bash
export ESP8266_BOARD=1
export FLASH_4MB=1
export ESP8266_SDK_ROOT=/mnt/c/ubuntu/esp-open-sdk/sdk
export PATH=$PATH:/mnt/c/ubuntu/esp-open-sdk/xtensa-lx106-elf/bin/
export ESPHOSTNAME=espruino:88
make $*

The last lines output look like:

LD espruino_esp8266_partial.o
LD espruino_esp8266_user1.elf
LD espruino_esp8266_user2.elf
To disassemble: xtensa-lx106-elf-objdump -d -l -x espruino_esp8266_user2.elf
Sections:
Idx Name          Size      VMA       LMA       File off  Algn
  3 .text         00006cd0  40100000  40100000  00002f10  2**2
                  CONTENTS, ALLOC, LOAD, READONLY, CODE
  4 .irom0.text   0006ab94  40201010  40201010  00009be0  2**4
                  CONTENTS, ALLOC, LOAD, READONLY, CODE
To disassemble: xtensa-lx106-elf-objdump -d -l -x espruino_esp8266_user1.elf
xtensa-lx106-elf-objdump -d -l -x espruino_esp8266_user1.elf >espruino_esp8266_user1.lst
  4 -rwxrwxrwx 1 root root   2204 Sep 17 10:10 eagle.app.v6.data.bin
428 -rwxrwxrwx 1 root root 437140 Sep 17 10:10 eagle.app.v6.irom0text.bin
 12 -rwxrwxrwx 1 root root   9616 Sep 17 10:10 eagle.app.v6.rodata.bin
 28 -rwxrwxrwx 1 root root  27856 Sep 17 10:10 eagle.app.v6.text.bin
** user1.bin uses  476884 bytes of 491520 available

I'm not sure why you build is failing on the user1 target.