There is an expectation that your TMF should provide document identification and version history. TMF regulatory guidance suggests that metadata should include information about versions. It can be assumed therefore that you need to implement some kind of system that easily allows you to identify that a document has been superseded by another. There is no simple answer how you achieve this. Ideally, your eTMF solution will provide you with a feature that clearly shows the version number and allows you to easily see when a document has been replaced by another. If the system does not provide this, then annotating superseded documents in some way (like you described) may be an acceptable alternative. That process should be documented so that it is consistently applied.