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SQL 2008R2 - Relocate default instance ID root directory after install

Our standard build is to install binaries on C drive & Instance Root directory in f:\SQLSERVER during SQL 2008R2 install.
I have found a server that does not fit the 'standard build'  the default  instance root directory is D  - I know I can change the default for database locations after the install, but I actually want to relocate everything on D   to F -  with the introduction of the 'Instance ID ' in SQL 2008 is this easy to do i.e. follow standard system database & user database  relocation instructions or is there something else I need to consider in regards to the 'Instance ID' and registry keys .
My preference is to rebuild and restore user database - but the customer does not want any extended down time .  
Any suggestions would be appreciated.
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Avatar of DBAduck - Ben Miller
DBAduck - Ben Miller
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Majellao

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Thanks for your prompt reply and assistance  - you have confirmed what I originally thought.
Good luck.  It is worthwhile venture to have consistency.
Can I ask one more question - in the scenario you suggested  (would take full dump anyway prior to uninstall) if I detached the user database and moved the mdf/ldfs  to the new partitions- could I use attach  for for user databases after the install - or should I rely on restores from the backups - just thought it may be quicker
I would take a full backup, then I would detach the databases and uninstall and reinstall.  Then attach the databases.

If you have logins in the master that you want to keep, you could use the sp_helprevlogin out on the support.microsoft.com site and store them for creation later on.
Assitance Greatly appreciated - confirmed my initial thoughts on potential issues