If the changes which you are merging involve removing or adding some files, update -j will reflect such additions or removals.

For example:

cvs update -A
touch a b c
cvs add a b c ; cvs ci -m "added" a b c
cvs tag -b branchtag
cvs update -r branchtag
touch d ; cvs add d
rm a ; cvs rm a
cvs ci -m "added d, removed a"
cvs update -A
cvs update -jbranchtag

After these commands are executed and a cvs commit is done, file a will be removed and file d added in the main branch.

Note that using a single static tag (-j tagname) rather than a dynamic tag (-j branchname) to merge changes from a branch will usually not remove files which were removed on the branch since cvsnt does not automatically add static tags to dead revisions. The exception to this rule occurs when a static tag has been attached to a dead revision manually. Use the branch tag to merge all changes from the branch or use two static tags as merge endpoints to be sure that all intended changes are propogated in the merge.