Answer
From the Search Domains window: right-click the relevant search domain and choose Show Details, then from the detail view right-click and select Drop Search Index (refresh the window to confirm it shows dropped). Next, right-click and select Schedule Domain Activation, click Enable Schedule to go to the Task Schedule window, right-click and Run it, then click 'View background jobs for this task' and manually execute the resulting background job if it isn't already running. Once that completes, repeat the same detail-view steps and click 'synchronized,' then run and execute the resulting background job again the same way. Afterward, check the Search Domain's detail window again — the domain should show as activated, and the 'Not Synchronized Documents' column should read 0 once every document is properly synced.