According to your logs, it’s finding and cutting it:
2020-03-21T19:06:02 MCEBuddy.CommercialScan.Remover → Commercial Remove: Before removal file size [KB] 2,212,568.00
INFORMATION> 2020-03-21T19:06:02 MCEBuddy.CommercialScan.Remover → Removing commercials using CutTS ext → .ts
2020-03-21T19:06:02 MCEBuddy.CommercialScan.Remover → ParseEDL: Cut Segment Start:1004.450 End:1125.670 Action:0
2020-03-21T19:06:02 MCEBuddy.CommercialScan.Remover → ParseEDL: Cut Segment Start:1223.320 End:1637.570 Action:0
2020-03-21T19:06:02 MCEBuddy.CommercialScan.Remover → ParseEDL: Cut Segment Start:1738.750 End:1796.860 Action:0
→ ConvertCutListToKeepList: Keep segment Start:0.000 Stop:1004.450
→ ConvertCutListToKeepList: Keep segment Start:1125.670 Stop:1223.320
→ ConvertCutListToKeepList: Keep segment Start:1637.570 Stop:1738.750
→ ConvertCutListToKeepList: Skip end segment, too small Start:1796.860 Stop:1798.556
INFORMATION> 2020-03-21T19:06:02 MCEBuddy.CommercialScan.Remover → CutTS: Cutting commercials from video - segment 0
2020-03-21T19:06:20 MCEBuddy.CommercialScan.Remover → CutTS : Merged Segements size [KB] 1,464,169.00
2020-03-21T19:06:20 MCEBuddy.CommercialScan.Remover → CutTS : Total Expected Segements size [KB] 1,464,170.00
You may need to adjust your commercial detection and make it more aggressive, check this page for details: