Without more specific information, it's hard to offer a concrete suggestion.  But there was a support case last week that might be relevant.  There was a bug in AT 9.0 (fixed in 9.1) where AT would incorrectly think that its schema needed updating, so it would momentarily put itself into single user mode while updating tables.  Depending on how you are taking your backups, this might be the interference you are seeing.  If this is the case, consider upgrading to 9.1.

As for scheduling service restarts, using the Windows scheduler seems like the easiest way.  The command lines "net stop lfaudit" and "net start lfaudit" should stop and start the service.

I would like to know if I use the "net stop lfaudit" as was suggested to fix my problem, will it stop only the data base writing or all the audit services? and if all is there any command that can stop only the db writing?

The audit service is responsible for both writing to the reporting database and generating reports for the web interface, so the reporting web interface will not be available.  Writing to the audit logs is the responsibility of the Laserfiche server, so that will continue as normal.  When the audit service is restarted, it will pick up where it left off and import any events that occurred during the down time.