Google Indexing API is a legitimate tool provided by Google to help website owners notify Google about new or updated content. It's designed to improve the speed and efficiency of the indexing process and should not harm your website if used correctly.
That being said, there are many factors that can affect your search engine rankings, and the use of the Google Indexing API may not necessarily be the cause of any issues you experienced with your sites disappearing from the SERPs. As you mentioned, the sites in question were PAA sites, and there could have been other factors at play that contributed to their disappearance.
If you are considering using the Google Indexing API again, it's important to ensure that your website is optimized for SEO and that you're following best practices. Additionally, it's important to monitor your search engine rankings and website performance closely after using the API to ensure that there are no negative impacts on your website.