Can a Server install alter a Time Machine backup's permissions?

I'm trying to change a server from Advanced to Simple, so I'd planned to:
1) Run a final Time Machine backup
2) Shut the server down
3) Reinstall Leopard Server from scratch
4) Reinstall any/all needed apps or files using Time Machine.
The first snag I ran into was that after step 3) all files in the Time Machine backup seemed to have had their permissions altered so that I could not access the folders and could not make changes to the files.
Based on help from someone else I was able to find out that an ACL is in effect on these files.
I also had some files stored on the Time Machine Backups drive as regular files....these do not appear to have the ACL applied.
When I couldn't figure out how to deal with that I went ahead and did a Full Restore using the Leopard Server Install DVD. This went without a hitch and the Time Machine backup files no longer appeared to have the ACL applied.
So can installing Leopard Server using all defaults where possible (excl. server name and such) and using the Simple server options alter the existing backups on a Time Machine Backups disk like this? Is there something I can/should be doing differently to get this to work "correctly"? Reinstalling from scratch again is still an option if there's something different to try.
Thanks in advance!
-Matt
P.S. I was expecting to have to do some manual reconstruction on the mail server that runs on this box, but didn't expect issues like this so any help is appreciated!

Hi, if I understand correctly yes, but may I ask the purpose of doing so?

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