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Hi Lakshmi, You're setup is being a bit troublesome. It is a bit frustrating when everything you try fails, I have been there many times :)

The flush is done just before the hotspot is activated so that part should be ok.
wpa_cli terminate >/dev/null 2>&1
ip addr flush "$wifidev"
ip link set dev "$wifidev" down
rm -r /var/run/wpa_supplicant >/dev/null 2>&1

The line that would clear the issue is sudo rm -r /var/run/wpa_supplicant

when wpa_supplicant is running it puts a file called wlan0 in that location. This is what is the feedback refers to.

The log you show has errors for IPv6, I believe that is expected as the RPi networking is setup for IPv4. Though realvnc is showing an error. While getting your access point running I would disable realvnc in raspi-config then enable it again once your up and running.

If the RTNETLINK error is happening like this i'm wondering if you have wpa_supplicant running more than once.
Can you confirm which Hotspot article you are following, I know your interested in have an internet hotspot and you are using ip but this article your commenting on is the non internet hotspot.
Just want to confirm you haven't taken config from both articles which would cause issues.

Can you confirm that you have updated your setup to the latest guide that was updated about two weeks ago.

Your /etc/network/interfaces file should contain no reference to wlan0 and should effectively be empty of device config.
Then /etc/dhcpcd.conf should have 1 line added, interface wlan0
/etc/dnsmasq.conf should contain this reference dhcp-range=,,,12h

Also you previously wanted to set this on a PI3 with a usb wifi dongle? are you setting this up on the internal wifi, wlan0?

when you manually run /usr/bin/autohotspotN what feedback is it giving?

If you are continuing to have issues you are welcome to email me your config files , hostapd.conf, dnsmasq.conf, interfaces, dhcpcd.conf, wpa_supplicant (remove passwords), autohotspot.service, autohotspotN
and any other information and I can have a look on my Pi3. email admin@ this site.