Subject to any file versioning rules when a component installs
it will overwrite resources.
A file resource normally follows various version rules to decide
if it should be overwritten.
The "RemoveFile" command or a custom action
can be used to clear files/folders, for example to force
an always overwrite behaviour.
The "COMPANY.MMH" header will (by default) update the "REINSTALLMODE" property so that files are overwritten irrespective of "normal" versioning rules, if you do not want this then reconfigure this behaviour. A major Windows installer limitation is that you can't be more selective (at a component or file level).
One or more custom actions to perform all the update and removal logic.