What I did:

1- SRC-WAN#show rom-monitor r0 to know bootstrap version

System Bootstrap, Version 15.4(3r)S5, RELEASE SOFTWARE

Copyright (c) 1994-2015 by cisco Systems, Inc.

2-SRC-WAN#sh platform to know chassis type.

Chassis type: ISR4331/K9

Slot Type State Insert time (ago)

--------- ------------------- --------------------- -----------------
0 ISR4331/K9 ok 05:32:13
0/0 ISR4331-3x1GE ok 05:31:12
1 ISR4331/K9 ok 05:32:13
R0 ISR4331/K9 ok, active 05:32:13
F0 ISR4331/K9 ok, active 05:32:13
P0 PWR-4330-AC ok 05:31:49
P2 ACS-4330-FANASSY ok 05:31:49

Slot CPLD Version Firmware Version

--------- ------------------- ---------------------------------------
0 15030325 15.4(3r)S5
1 15030325 15.4(3r)S5
R0 15030325 15.4(3r)S5
F0 15030325 15.4(3r)S5

3-copy ftp://mmr_ops:Pa$$word2020@10.1.81.50/isr4200_4300_rommon_169_1r_SPA.pkg
flash:

4- upgrade rom-monitor filename bootflash:isr4200_4300_rommon_169_1r_SPA.pkg all

5- copy ftp://mmr_ops:Pa$$word2020@10.1.81.50/isr4300-universalk9.16.09.03.SPA.bin
flash:
[OK - 583810543/4096 bytes]

583810543 bytes copied in 253.463 secs (2303336 bytes/sec)

SRC-WAN#

6- config t
no boot system flash isr4300-universalk9.03.13.04.S.154-3.S4-ext.SPA.bin
boot system flash isr4300-universalk9.16.09.03.SPA.bin

7- reload

8- check your bootstrap version and ios version after upgrade. Use the below
commands:
Check bootstrap version: sho rom-monitor r0 and show platform
Check IOS version : show version

In case system keeps boot from old ios, then use: software install file
flash:isr4300-universalk9.16.09.03.SPA.bin

My Verification:

SRC-WAN#sh rom-monitor r0
System Bootstrap, Version 16.9(1r), RELEASE SOFTWARE
Copyright (c) 1994-2018 by cisco Systems, Inc.

SRC-WAN#sh vers
Cisco IOS XE Software, Version 16.09.03
Cisco IOS Software [Fuji], ISR Software (X86_64_LINUX_IOSD-UNIVERSALK9-M), Version
16.9.3, RELEASE SOFTWARE (fc2)

SRC-WAN#show bootvar
BOOT variable = isr4300-universalk9.16.09.03.SPA.bin,1;
CONFIG_FILE variable does not exist
BOOTLDR variable does not exist
Configuration register is 0x2102

Standby not ready to show bootvar

9- Keep old IOS saved in ftp server:

copy flash:isr4300-universalk9.03.13.04.S.154-3.S4-ext.SPA.bin ftp://mmr_ops:Pa$

$word2020@10.1.81.50

10 - Keep the current running-config in the ftp server:

copy running-config ftp://mmr_ops:Pa$$word2020@10.1.81.50

Enable secret type 8:

R1(config)#enable algorithm-type sha256 secret cisco
R1(config)# username fabbas algorithm-type sha256 secret cisco

Enable secret type 9:

R1(config)#ena algorithm-type scrypt secret cisco
R1(config)# username fabbas algorithm-type scrypt secret cisco