Act Governing Relations with Hong Kong and Macau Article 14-2

Any resident of Hong Kong or Macau Area who overstays the authorized duration of residency in the Taiwan Area for less than thirty days and whose original basis of application for the residency still exists may re-apply with the National Immigration Agency of the Ministry of the Interior for residency after being penalized pursuant to Article 47-1. A period of one year shall be deducted when calculating the required duration of stay or residency in the Taiwan Area.
中文原文 香港澳門關係條例第14-2條
香港或澳門居民逾期居留未滿三十日,原申請居留原因仍繼續存在者,經依第四十七條之一規定處罰後,得向內政部移民署重新申請居留;其申請定居者,核算在臺灣地區居留期間,應扣除一年。

English translation for reference only; the Chinese text prevails. Not legal advice.