A reduced service ran between Chester and Llandudno Junction with buses supplementing services.
Buses replaced trains between Llandudno Junction and Blaenau Ffestiniog.
There was also a warning that services between Llandudno Junction and Holyhead could have been affected by the work.
Services have resumed on the north Wales coast main line and Blaenau Ffestiniog branch line after earlier disruption on Monday when engineering work overran.