I am trying to do an incremental upgrade on a site and first step is from 4.0.3 to 4.4.1

The install script ran fine except the very first error:

00:00:00.917 - Upgrading to Version: 4.0.4 Error! (see C:\projects\ASP.NET\dotnetnuke\Providers\DataProviders\SqlDataProvider\04.00.04.log for more information)

And the log said:

System.Data.SqlClient.SqlException: The ALTER TABLE statement conflicted with the FOREIGN KEY constraint "FK_Files_Folders". The conflict occurred in database "datadnn", table "dbo.Folders", column 'FolderID'.
   at System.Data.SqlClient.SqlConnection.OnError(SqlException exception, Boolean breakConnection)
 

The updated site appears to work fine but wonders what area is likely broken because of this.  Is it possible to re-run the install script again and if so, how can I trigger it.  Thanks in advance.

Do I copy the content of the sqldataprovider file to the input box and then execute the input content as script?  I don't think it has the option to run the script file directly.  If I run it manually in the input box, I need to replace all instances of  {databaseOwner} and {objectQualifer}.  I don't think objectQualifier is set in my web.config file.  And I seem to run into lot of syntax error if I replace databaseOwner as "dbo" and objectQualifier as blank.

I re-synced the folders and re-run the 4.0.4 script but ran into other SQL problems.  I don't recall but it is compalining something like duplicated column name "RSVPCode" in dbo.roles.  Sound like I cannot simply rerun the script as some tables may have been updated during the initial upgrade process?

I rolled back to 4.0.3 and realized the file sync buttons are not available in this version.  I tried to upgrade to 4.4.1 and it failed on 4.0.4 script as expected.  My question is: is there a way to pass 4.0.4 script by simply running the upgrade process without any manual work at all?

Tonight I'll try to upgrade to earlier version first and funny thing I see in SourceForge.net, the next version up from 04.00.03 is a big jump to 04.03.00. For example, there is no 04.00.04.  I have a feeling it will fail at the same spot even if I try to upgrade to 4.03.00. 

Also, should I upgrade using the install or the upgrade packages?  I have been using the Install package, if it does matter...

Any help is appreciated.