If I had to guess, it is probably something to do with the qualcomm drivers not finding the modem after easyflash resets the modem... I have not tried this on a MKR NB1500 yet, so I cant help more... Here is the log from my update in the Mikroe modem:
Using USB port
Processing 'SARA-R410M-02B-03-L0.0.00.00.05.12_A.02.19_IP.dof'
Please TURN ON the device and don't disconnect power supply
Waiting for device...
Device found!
Mobile Version report: PASS
Ext Mobile Mobile SW Rev: L0.0.00.00.05.11
-> Backup of legacy NV objects
Process time was 20.3 sec.
OK
-> Backup of ublox legacy NV objects
Process time was 125 msec.
OK
-> Backup of RF NV objects
Process time was 7.6 sec.
OK
-> Backup of CONF NV objects
Process time was 5.0 sec.
OK
-> Backup of FS objects
Process time was 0 msec.
OK
-> Backup of Alternate FS objects
Process time was 15 msec.
OK
-> Switching to download mode
Waiting for synchronization...
<1>
Device synchronized.
Injecting NPRG9x06.mbn
Boot-loader is active
-> Partition table '0:MIBIB' from 'partition.mbn' loaded!
Process time was 6.4 sec.
OK
-> Start downloading item '0:EFS2' from 'efs.mbn'
Process time was 2797 msec.
OK
-> Start downloading item '0:sec' from 'sec.dat'
Process time was 15 msec.
OK
-> Start downloading item '0:TZ' from 'tz.mbn'
Process time was 1313 msec.
OK
-> Start downloading item '0:MBA' from 'mba.mbn'
Process time was 594 msec.
OK
-> Start downloading item '0:ACDB' from 'acdb.mbn'
Process time was 296 msec.
OK
-> Start downloading item '0:RPM' from 'rpm.mbn'
Process time was 360 msec.
OK
-> Start downloading item '0:QDSP' from 'qdsp6sw.mbn'
Process time was 56.1 sec.
OK
-> Start downloading item '0:APPS' from 'apps.mbn'
Process time was 11.6 sec.
OK
-> Start downloading item '0:UA' from 'UA9x06.mbn'
Process time was 421 msec.
OK
-> Start downloading item '0:EFS2BKUP' from 'padded_efs.mbn'
Process time was 2407 msec.
OK
-> Start downloading item '0:EFS2APPSBKUP' from 'efs2.mbn'
Process time was 703 msec.
OK
-> Start downloading item '0:EFS2APPS' from 'efs2.mbn'
Process time was 734 msec.
OK
-> Start downloading item '0:SBL' from 'sbl1.mbn'
Process time was 516 msec.
OK
Resetting device...
Device found!
WARNING service interface locked!
-> Restore of legacy NV objects
Process time was 407 msec.
OK
-> Restore of ublox legacy NV objects
Process time was 78 msec.
OK
-> Restore of RF NV objects
Process time was 8.1 sec.
OK
-> Restore of CONF NV objects
Process time was 2641 msec.
OK
-> Restore of persistent objects in FS
Process time was 0 msec.
OK
-> Restore of persistent objects in Alternate FS
Process time was 0 msec.
OK
-> Apply SCR objects
Process time was 15 msec.
OK
Mobile Version report: PASS
Ext Mobile Mobile SW Rev: L0.0.00.00.05.12
Extra command: RESET
Process time was 0 msec.
OK
Process time was 2 min 29 sec.
Done!
Please TURN OFF the device and press 'Start' to install the firmware