Mass upgrade APs

Hello!
We have a couple thousands brand new cAPGi-5acD2nD with firmware 6.44.5
About 10-20 AP installation and setup per day very very distracting. And decided to make some script for update.
Firstly - We don’t want to upgrade via WAN network.
Second - Less attention for this process.
So couldn’t think of anything better than download 6.46.4 firmware via curl to the root of the default-open FTP service on Mikrotik.
Further generate some config.auto.rsc with last line “/system reboot” and also download to FTP Mikrotik.
Config applies perfectly, but no upgrade after reboot and no firmware file on the root. With manual reboot all works fine and system upgrades.
Any Ideas what is wrong with upgrade while reboot?
Default out-of-the-box config:

/interface bridge add admin-mac=C4:AD:34:7E:B2:7C auto-mac=no comment=defconf name=bridge
/interface wireless set [ find default-name=wlan1 ] band=2ghz-b/g/n channel-width=20/40mhz-XX disabled=no distance=indoors frequency=auto installation=indoor mode=ap-bridge 
ssid=MikroTik-7EB27E wireless-protocol=802.11
/interface wireless set [ find default-name=wlan2 ] band=5ghz-a/n/ac channel-width=20/40/80mhz-XXXX disabled=no distance=indoors frequency=auto installation=indoor mode=ap-b
ridge ssid=MikroTik-7EB27F wireless-protocol=802.11
/interface wireless security-profiles set [ find default=yes ] supplicant-identity=MikroTik
/interface bridge port add bridge=bridge comment=defconf interface=ether1
/interface bridge port add bridge=bridge comment=defconf interface=ether2
/interface bridge port add bridge=bridge comment=defconf interface=wlan1
/interface bridge port add bridge=bridge comment=defconf interface=wlan2
/ip dhcp-client add comment=defconf dhcp-options=hostname,clientid disabled=no interface=bridge
/system clock set time-zone-name=Europe/Moscow
/system routerboard mode-button set enabled=yes on-event=dark-mode
/system script add comment=defconf dont-require-permissions=no name=dark-mode owner=*sys policy=ftp,reboot,read,write,policy,test,password,sniff,sensitive,romon source="\r\
    \n   :if ([system leds settings get all-leds-off] = \"never\") do={\r\
    \n     /system leds settings set all-leds-off=immediate \r\
    \n   } else={\r\
    \n     /system leds settings set all-leds-off=never \r\
    \n   }\r\
    \n "

Our generated config:

/interface ethernet set [ find default-name=ether2 ] disabled=yes
/interface bridge port add bridge=bridge interface=all
/interface wireless security-profiles
add authentication-types=wpa2-eap group-ciphers=tkip,aes-ccm management-protection=allowed mode=dynamic-keys name=SHOP-RADIUS supplicant-identity="" unicast-ciphers=tkip,aes-ccm
/interface wireless set [ find default-name=wlan1 ] antenna-gain=0 band=2ghz-g/n country=russia disabled=no distance=indoors frequency=auto installation=indoor mode=ap-bridge name=2.4 security-profile=SHOP-RADIUS ssid=SHOP wireless-protocol=802.11 wmm-support=enabled wps-mode=disabled
/interface wireless set [ find default-name=wlan2 ] antenna-gain=0 band=5ghz-n/ac country=russia disabled=no distance=indoors frequency=auto installation=indoor mode=ap-bridge name=5 security-profile=SHOP-RADIUS ssid=SHOP wireless-protocol=802.11 wps-mode=disabled
/radius add address=10.0.17.99 secret=WIFISECRET service=wireless
/radius add address=10.177.0.82 secret=WIFISECRET service=wireless
/radius add address=10.0.19.38 secret="LOGINSECRET" service=login
/radius add address=10.0.7.29 secret="LOGINSECRET" service=login
/user aaa set use-radius=yes default-group=full
/interface wireless enable [ /interface wireless find ]
/system routerboard mode-button set enabled=no
/ip service set telnet disabled=yes
/ip service set ftp disabled=yes
/ip service set www disabled=yes
/ip service set api disabled=yes
/ip service set api-ssl disabled=yes
/ip dns set allow-remote-requests=no
/tool mac-server mac-winbox set allowed-interface-list=all
/system clock set time-zone-name=Europe/Moscow
/system ntp client set enabled=yes primary-ntp=10.253.0.4 secondary-ntp=10.253.0.7
/user aaa set accounting=no default-group=full
/user set [find name=admin] password=PASSWORD
/ip address add address=10.50.28.187/26 interface=bridge
/ip route add dst-address=0.0.0.0/0 gateway=10.50.28.129
/system reboot

Since we are talking about Access Points, i guess you use CapsMan as well…
So through CapsMan you can force all the Caps APs to update by setting on the CapsMan the upgrade policy to “require-same-version”… (Capsman must be upgraded !)
https://wiki.mikrotik.com/wiki/Manual:CAPsMAN

Also if you use Dude you can do it through there as well from the comfort of your Office…
https://wiki.mikrotik.com/wiki/Upgrading_RouterOS_with_Dude

Just pointing some alternatives…

No, No CapsMan and no Dude.
All I need is understand why after downloading .npk file to the AP and reboot it via xxxx.auto.rsc downloaded command it removes file from flash and performs no upgrade.
Maybe I should do some extra command.

I suspect you have discovered another user-interface pessimization caused by the new update mechanism introduced in 6.46.2. You can read much about it here, keep searching for posts containing the words “hidden” and “hide.”