Atlas.ti by default doesn't change your source files, but automatically makes copies, though you can deviate from it by using "linked media files".
Regularly make snapshots (a kind of "Save As") of your projects. That's how you keep different 'milestones' in your project clear and ready to go back to.
The files of your projects are by default stored in the so-called library, a hidden directory on your device.
It is possible to put this library (or multiple to switch between) in a different location, also on a server. But be careful with cloud-based services like for example Google Drive, DropBox, or what many people are using without being aware: OneDrive; the automatic backup/synchronization can wreak havoc on the consistency of your projects. With Saxion's Research Drive it should under restrictions be possible if you directly map your library on that drive. Restrictions because as soon as multiple devices or users are involved you might run into (synchronization) issues. Since version 23 of ATLAS.ti there's also a cloud version, but first make sure your data is allowed to go there. If allowed, it's good to know it also has a real-time "live" cooperation mode from within the ATLAS.ti web version. For proper backups and being able to work with multiple versions/software/devices/users export so-called bundles. The project bundle (previously "copy bundles" or "transfer bundles") keeps the full data for further editing in ATLAS.ti.
Project bundles from older atlas.ti versions can be opened and will then be automatically converted to the version of the current version in use. When multiple users have separately worked on a project, Merge can be used to combine the result.
The special QDPX project bundle is for exchange with other Qualitative Data Analysis (QDA) tools and long-term archival.