Cannot use APIs for Data Refresh in PBIS

We are using APIs in PBIX to get data and the refreshes work. When we upload to PBIS to run and refresh out models in the cloud, the same APIs and M Queries do not work for all our APIs, specifically those with multiple query parameters in the APIS. We are an ISV and we want to have multi-tenant (workspace) architecture and refresh our models multiple times a day. We need APIs on scheduled refresh. Some APIs work (we had to put all relative paths in the main URL), but some cannot connect based on security/truest authentication. Please have the engineering team review API protocols in PBIS. Thank you.