As far as I know, planning a new route should not overwrite an existing activity recorded with the Tracker. Activities and planned routes are stored separately, so even if you started planning a new route while viewing the recorded activity, the original recording should remain unchanged.
Are you sure the recording was saved successfully and appeared in My Maps → Activities afterwards?
Unfortunately, Mapy.com does not currently have a recycle bin or a feature for restoring deleted items. If the activity is no longer visible either in the app or on the website, there is no way for you to recover it yourself. Mapy.com does not restore deleted items either, as they do not interfere with the contents of users' accounts.
The only way to back up your recordings is to export them as GPX files and keep those files somewhere safe. If an activity is accidentally deleted from My Maps, you can import it again from the saved GPX file.
One more thing comes to mind: are you signed in to the same account you were using when you saved the recording? Recordings don't normally disappear on their own, so perhaps it was saved under a different account.
Finally, if you remember exactly where you went, it is possible to recreate the activity manually, assign start and end times, and import it into your Mapy.com account as an activity. If you'd like to try this: gpxmapy.cz – EN version > fast functions > other steps > creating an activity
