"Lynx" stood in to San Francisco Bay on 6 May 1944, and anchored. Underway two days later, she moored at Pier 25, San Francisco, on 8 May, where she began a period of minor repairs and alterations in the hands of the General Engineering Co. on 9 May. Shifting to the General Engineering & Drydock Company's yard at Alameda, on 16 May, she entered the floating dry dock , where her bottom was scraped and painted and paravane gear installed, 16–19 May. Underway once more on 20 May, "Lynx" fueled at the Point Orient Fuel Dock that same day, then put into Port Chicago to load cargo at the Naval Magazine there 20–28 May. Shifting to Pier 92, San Francisco, on 28 May, she continued to receive minor repairs and alterations through the end of the month, such work being completed on 31 May, when she also completed loading her holds. She completed loading deck cargo, "LCT-1096" and five re-arming boats, on 1 June, then proceeded to the Tiburon anchorage, San Francisco Bay, on 2 June.