I have fixed the number in your post. Latest version is 4.1.3.
Depends on your OS and used installation method. Usually one just have to stop Openfire (or its service) and then install on top of it. Doing a backup before that is always a good thing.
I made copy of full folder where version 4.0.3 was installed.
Made the update. Service is starting but clients do not connect.
Where the main base in folder is?
How to copy old base (embedded-db) to new installation?
Update doesn't delete or overwrite the current database. Just updates its scheme if needed. You can copy old database over, but it might not change anything. Are you able to login to Admin Console after the update and see the users and groups?
Embedded-db folder is inside Openfire installation folder. On Windows it is in Program files\Openfire folder, but you haven't mentioned what OS you are using Openfire on.
The OS is Windows 2008r2 x64.
I uninstalled the old one.
Installed new version with java.
Put the database back in installed program files. Service is started.
But I can not go in to admin console and the clients can not join the server.
The server reboot or service restart do not change situation.
The base size is 900Mb. I think the base is broken.
How can I repair it or how to make new base with old accounts (because of the big number of accounts)?
Check the all.log at Openfire/logs folder and look for recent errors.
That database is indeed very large. Unless you were saving chat history and it was running for many years with lots of users.
If you are using LDAP integration, you can setup it again and pull the users from AD. If not, then you will have to create all the users again.
Do you have full backup or only the database? Maybe it would be more convenient to restore old installation and test uograding on some test server. Or you can download the version you were using (by replacing version number in the download link), install it and put the database backup.