Active jobs will continue to run.
In adTempus 4, hold/release is a group-level (or queue-level) operation (in previous versions, holding a group really just held every job in the group individually). Holding the group overrides the hold settings for all jobs in the group, but when you remove the hold on the group, the jobs have their original hold state. Shorter answer: yes.
While a job is held, adTempus stops evaluating triggers. For a file trigger, if the file is still there when the job is released, it will trigger (because the trigger works by scanning the folder, not by watching for events). But if, say, the file was created and deleted before the job is released, it will not cause a trigger, because adTempus will never see it.
I need to revise my original answer. In your case "Disable all execution" is probably not what you want because that will also prevent chained jobs from being kicked off (by Responses). Since you want your job stream to keep executing, you probably want to choose the "Custom" option and then choose "Hold triggers" and "Prevent manual execution" but leave chained execution enabled. However, if you're using Job Triggers to link your chain together, you're stuck, because holding triggers will disable job triggers, so your chains cannot run. We maybe should be treating job trigger differently here.