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I know NS update could take over 24h. However during this process there is something that intrigues me.

I can't change ISP router's DNS so I set WAN/LAN to use Google Public DNS

The process scenario:

1. I change a domain NS


2. After some minutes, I go to dnschecker.org , I add a custom DNS Server to enter Google public nameservers


3. 
   dnschecker.org let's say it lists 50% of DNS updated servers including Google DNS


4. I go to windows command line and enter ipconfing /flushdns
   


5. I clear all chrome file cache (Ctrl+Shift+Del), clear chrome host (chrome://net-internals/#dns) cache and flush chrome sockets pool ( chrome://net-internals/#sockets )


6. Finnaly I open the website in new Chrome (or other browser) window tab, and the displayed website is the old one. However, at the same time, if I access the domain through some free online proxy like Whoer, the website loads the updated DNS version.


7. Only 24 hours later my chrome loads the updated DNS site version.

How could that be? Am I missing something?

The DNS server of your ISP has your address in its cache, and so is returning
the old address. It will keep on doing so, until the
Time To Live (TTL)
of your data will expire.

DNS records are stored in cache, mainly to improve performance of DNS queries.
Every DNS record has a Time to Live (TTL) value, which is the time DNS servers
should store that record in cache. Even if a record is changed, DNS servers
will continue working with its former value from the cache until this time has passed.

DNS propagation is the time required for DNS servers worldwide
to update their cached information for a domain name.
It is influenced by the TTL of DNS records that might have changed,
but there are also other factors that could come into play.

A DNS change may require up to 72 hours to propagate worldwide,
although most often this happens in a matter of hours.

To speed up the propagation time is possible by having your TTL set to a
lower number (not recommended), for example 14400 (4 hours).
But you should do that well before the NS change, maybe as much as
96 hours in advance.

When you query a DNS server that does not have your DNS in its cache,
you might find that it returns the new DNS record, if the change
has already propagated that far.

As you noted, you are using your ISP's router, and it appears to be set to use only the ISP's DNS servers.

Meanwhile, you've used the website to check Google's DNS servers. You could infact do this on your local machine too – nslookup <domain> 8.8.8.8 in a command prompt will query 8.8.8.8 for the IP of <domain>.

What you're seeing is that most DNS servers on the 'web' have updated, yet your ISP's DNS server is still returning the OLD result, and will continue to do so until it updates. You can bypass this issue by simply not using your ISP's DNS servers, setting them manually on your machine (however, this will work only if your ISP isn't blocking external DNS access).

Once your ISP's DNS servers updated, you then receive the updated page, just like everyone else on the web will.