smnirosh
....I am stucked....
First of all your knowledge of sme server seems poor, so do not start doing procedures that you are unsure of or are guessing may have a satisfactory outcome.
LISTEN to the advice that the very knowledgeable people here are giving you, & slowly & completely read everything they have answered to you.
I think you are on the wrong approach trying to backup & do selective restore of files. You are likely to get your server in a much bigger mess & even an inoperative state if you restore files wrongly.
You would need to have a very good knowledge of sme server to know which files to restore to just get configuration information restored. Configuration data is held in numerous files, & some of that information correlates to data in other files, get them wrong, & your server may not work.
Note that you can safely run "Configure this server" anytime.
If you step through all the settings & do not change anything, & the system does a reboot, all your user data in ibays etc & email will still be there, these remain unchanged, even the configuration will remain unchanged, it is just that old configuration setting values will be replaced with the same new values.
As mentioned earlier by Charlie, you can see what changes you may have inadvertantly made, by going through the /var/log/messages log file, & review the configuration commands which will show OLD & NEW configuration entries.
It should be relatively straightforward to indentify any changes you made, if any were made.
If nothing changed, then the OLD & NEW settings will be the same.
Either way a reboot will not harm your server or the data it contains.
At worst you may need to re-run "Configure this server" & correct any incorrect setting, which are mainly relating to network connectivity & basic server settings etc.
If you backed out of the "Configure this server" process, then I would assume you have not changed anything (?)
Trying other procedures such as backup & selective restore will be much more difficult than just running "Configure this server" & making a correction.
Perhaps nothing has changed & there will be no unwanted effects after you reboot.
Please do not complicate your situation by doing other things that are not really warranted.
One thing for sure you should do first, is step through the "Configure this server" screens again, & write down every single setting & the current value displayed. It may take you 15 minutes, but at least you will have a seperate "paper based" record that you can refer to if necessary ie should you need to correct a inadvertantly or wrongly changed setting or two.
If there is a problem after the reboot that you are fearful of doing, then you can ask here for hints or tips regarding the correct setting choices, & advise us what the current settings are based on the written list you made.
THINK FIRST