Oracle enterprise manager showing wrong port after change
Sometimes it helps to de-install the enterprise manager and then re-install it using the emca command. We'll leave that for the worst case.

Using EMCA After Changing the Database Listener Port


  If you change the listener port of the database after you have configured Database Control, the database status will appear as down. To reconfigure Database Control so it uses the new listener port, run the EMCA command using the -config dbcontrol db [-cluster] command-line arguments.


(emphasis mine)

Reference: Enterprise Manager Advanced Configuration (Oracle Docs 10g)

In your case you would run the following commands:

SET ORACLE_HOME= your_oracle_home
SET ORACLE_SID= your_oracle_sid

emca -config dbcontrol db


You might have to provide various pieces of information when re-configuring the Enterprise Manager: 


port
SID
DBSNMP_PWD
SYSMAN_PWD
HOST_USER
HOST_USER_PWD
SYS_PWD


If this doesn't reconfigure the database control for your instance you might have to re-create the repository containing all the Entrprise Management Console configuration settings. You would achieve this be adding a parameter to the previous command:

SET ORACLE_HOME= your_oracle_home
SET ORACLE_SID= your_oracle_sid

emca -deconfig dbcontrol db
emca -config dbcontrol db -repos recreate


This will de-configure the EM Console settings for a database (not for a cluster installation) and then recreate the repository.

The additional information I listed above will be required for a re-configuration to work.


  DISCLAIMER
  Re-configuring the Enterprise Management Console is no easy task. I have failed many times (especially with broken timezone settings). If you are unsure or don't feel in the position to risk your installation, please consider contacting an Oracle Consultant.  
  
  If you have a test environment, consider trying this out there first.