Reset my root password, now I can't see my main database I was getting access denied for root@localhost. To resolve this, I stopped the mysql services, ran mysqld --install and mysqld --initialized, added skip-tables in the my.ini file and was able to log back in with the root user got the password to reset. Cleared the skipped-tables from the my.ini file. Flush the privileges, granted the root all access. Put in the command "show databases;" but it only shows these databases and its missing one.

information_schema
mysql
performance_schema
sys

I looked at the my.ini file to see where the datadir was, looked at the path and I see the folder and the ibd file where the database resides, but it still does not show in MySQL. Any help on this would be greatly appreciated.
MySQL --initialize installs a clean data directory. It seems like that's what you got.

There may be a previous idb file there but its not connected to the database.