Arabic became the spoken language of the Samaritan community, as it did across the region, and the community went on writing. Some of what it produced in Arabic is written in the Arabic script, and some of it is Arabic language in Samaritan letters, a practice with parallels in other communities of the region that kept their own scripts while changing their speech.
Writing one language in another language script is more common in the history of writing than it looks from a modern vantage point, where scripts and languages are usually paired one to one. It happens wherever a community has a script it regards as its own and a spoken language it shares with its neighbours. The script then marks who the text belongs to rather than what language it is in, and a reader outside the community may be unable to read a text in a language they speak fluently.
For the Samaritan alphabet this is the third language it has carried, after Hebrew and Aramaic, and it is the one that shows most clearly what the script is for. An alphabet of twenty-two consonantal signs is not a good fit for Arabic, which has twenty-eight consonants and needs more distinctions than these letters supply. Using it anyway is a choice about identity rather than about convenience, and it is the same choice, in a different century, that kept the community writing Paleo-Hebrew letters when everyone around it had moved to the square script.