@Perla Escarcega  - that is one of the ways to do a Refresh, yes.  You need to first populate all files in your Source Workspace, and then the Refresh will walk the directory contents and load everything in.

More details can be found on slides 43-45 of ICC520:

ftp://ftp.intersystems.com/isc/customers/ccrtraining/ICC520(Presentation)%20CCR%20Tier%201%20-%20Baselining%20Source%20Code.pdf
 

@Perla Escarcega  - taking a closer look at this, I think we had an issue with a historical file clean-up routine which was a little too overeager to reclaim space.  All of your source is safe and available but you may need to create a fresh ItemSet to push this source.  Note - you should always be making fresh ItemSets anyway because the head revision may be newer than what is in your historical ItemSet, and you don't want to get an older revision of something which breaks when interacting with a newer revision of other items.  So simply create a new ItemSet for BASE and deploy it and you should be all set.

P.S.  This does raise the question of why you are initializing a new Secondary BASE environment from old ItemSets as opposed to just grabbing the head revision of the BASE source and running Refresh to pull it all into the Namespace?  I am afraid your approach may be significantly more risky than the recommended approach.  

@Perla Escarcega  - the fact that it is already in LIVE should not have any bearing here.  I am guessing that the newly created Namespace is part of a newly created instance?  It looks like you may have an older version of the CCR Client Tools with a bug in it.  Could you provide the results of "Do Version^%buildccr" so we can see what versions of the tools you are running?