Unity tracks both time settings and the actual time in its TimeManager object. In the editor, updating the TimeManager.asset externally while in play mode will cause the TimeManager to be reloaded from disk, not just updating the time settings but also resetting the current time.

Arguably, time settings should be tracked separately from the current time, enabling one to be reloaded without affecting the other. However, that is unfortunately a decidedly non-trivial change with a high risk of introducing bugs in other systems (since just about every subsystem depends on time).

Considering that this bug is only an issue in the editor and affects very few users, we've decided not to fix it at this time, though it's likely to eventually be fixed as part of larger, long-term architectural changes.

Steps to reproduce:

1. Open attached project "826269.zip"
2. Make sure that Preferences > General > Auto Refresh is enabled
3. Open scene "Test" and run it
4. Notice time counting
5. Externally, open TimeManager.asset file and save it to change file timestamp
6. Return to editor and notice that Time.time got reset to 0

Expected result: only change Fixed Timestep, Maximum Allowed Time and Time Scale

Reproduced with: 5.2.5f1, 5.3.6p2, 5.4.0p3, 5.5.0b1