After struggling from weeks and chatting with my hosting support team I found below solutions.
The below solution is for if Blogengine is installed in root directory
1) Correct the admin URL
Instead of this URL
Use this URL
2) Check Custom handlers working or not
Right click on browser and select "View page source" of your blog
In html source find and click on any .axd file eg.: admin.res.axd, syndication.axd etc...
If .axd file not open in browser or giving 404 error do below steps:-
Remove <handlers> from <system.webServer> but keep <httpHandlers> in <system.web>
3) Check Application Pool
If it is Integrated change it to Classic
If it is Classic change it to Integrated
Above these 3 solutions will definitely solve your problem.
Happy Blogging with Blogengine.net
To avoid conflict and get the latest code from git repository and then start your changes use below 2 commands in order as below:-
git reset --hard HEAD