Resilio Connect Management Console allows to remotely disconnect an agent and thus remove it from all jobs. 
Understanding what happens next comes from knowing how agent is authorized on MC - using bootstrap token and client token (read more).
Files removal
When removing agent from MC, mind parameter "Keep folder data" in Agent profile as it may force agent to remove files which were part of the job. Starting with version 2.12 files remain on disk regardless.Here's what happens when admin deletes an Agent from the Console
Agent's client_token is erased from MC records and the agent is not authorized anymore.
Agent ID and name are added to the blocked agents' database and the agent will not connect to the MC anymore, until it's recovered from this database (see below).
Here's what will happen with other MC's components:
License
The agent will free up one seat of its package in the license.
Jobs
Agent will be removed from jobs. So if the removed agent was the only source in a Distribution or Consolidation job, the job run will give the error "There are no source agents".
If reconnected, the Agent won't rejoin the job unless auto sorting of groups is enabled. Admin shall manually add the agent to all the jobs. Note, that the agent won't continue interrupted distribution or consolidation job run automatically.
Groups
Removed agent will be also removed from its groups. The Agent will rejoin the group if group sorts agents by tags.
Removing Management console agent
If admin accidentally removed the Management console agent, please contact support.
Removing agent from the agent's side
Stop agent process and delete its storage folder.
How to reconnect a deleted Agent
For MC v3.2 and older, It's not possible to reconnect a deleted Agent. Proper way to do it is to uninstall* the agent, clearing its storage folder, and initiate new connection again. The agent will generate new Agent_ID and connect as a new agent with a different client_token.
If you removed agent(s) accidentally from the MC and it's not connecting anymore, or reinstalling the Agent is not a feasible option for your workflow, please contact Resilio support team to work on a possible solutions.
For MC v 3.3.0 and newer, while the option with reinstalling is still valid, it's now possible to avoid it and restore the deleted agents right from MC - from drop-down menu "Removed Agents". The menu is available for Admins and MC users who have full access to Agents.
This is a list of deleted Agents. While the Agent is listed in this table, it won't be able to reconnect to MC, until it's removed from the list. All its connections will be declined. Select an Agent or multiple Agents and click Recover.
Recovering an Agent is basically clearing it from the list of "blocked" Agents. Recovering the Agent does not automatically reconnect the Agent to MC again! The Agent shall initiate the connection to MC so as to reconnect - restart of the Agent is required.
If the Agent uses a configuration file, it will automatically reconnect after restart. If the bootstrap token the config file is incorrect, the Agent will request approval. If admin declines the Agent now, it's declined for good without possibility to restore it, reinstall will be required.
If the Agent connects to MC without config file (using MC address only), the Agent will require approval. If admin declines the Agent now, it's declined for good without possibility to restore it, reinstall will be required.