That is interesting - Gold/Platinum never stated there would be a problem running the commands with the DB up.
Haven't had any problems with good objects being removed or groups of them by using the sbadmcl -cleanupxgroup. Have had probably 3 or 4 dead objects found in the past 6 months of using the commands and those were sometimes prompted to be done because we couldn't pull up the properties of an object in the DB or reset a group to the configuration.
We have per machine about 8 users assigned to them max - I think support believes we are adding our 3000 user group to every machine hence their reluctance to help me unless I "break the groups into 500 or less increments"... which to me is ridiculous. What do larger enterprises do when they have 100K+ objects... break them into 5000 different user groups or machine groups? Somehow I doubt it...
We also have a very robust dedicated physical server that exceeds ALL of the spec recommendations.
I strongly second that recommendation. It will definetely cause damage if they are active user connections to a database. Make sure that script is run to a local database and other communication/database services are turned off. Better yet, run them on a recent copy of production database, to see potential effects first, before you run it on production system