I've found related info about downloaded maps in Collector documentation-for-versions-and-replicas-created-by-collector and some esri documentation but it doesn't quite answer my question. We don't use Collector to make field edits, essentially only for navigating with GPS enabled devices, as we're in areas without cell coverage. We don't need to synchronise any changes back to the default SDE and so over a long period of time each of these versions has just stayed where it is, many of which are months old.
I just want to ask if there might be any issues caused simply by deleting these created versions rather than synchronising them back, considering how out of date they might be now.
Deleting an offline area from Collector should create a call to REST to delete the replica the next time a connection is established. Sometimes you may be in a state where you cannot delete the map from the device because the device is unavailable, locked, or any other reason. As long as you have already synced any changes in the data or recovered the database directly you should be safe to manually delete any replicas or versions.
Based on your description of your workflow, it sounds like you may be better suited using Explorer for ArcGIS as you are not making field edits. Explorer also allows for Offline maps and GPS locations (no external GPS support).
That's an interesting idea about using Explorer instead of Collector, and one i will look into. Because we don't actually make changes to the data i don't think anyone actually syncs back to the device, only just deleting whatever copy of the webmap was downloaded when not required. This is especially true for our live Production database, which is not edited but has 100+ versions from different users.
For now I'll clean up as best I can which may not be following best practice but something to correct in future.