Hello,
There's no option to remove /F1, /F2, /F3 elements from the conversion. These elements are needed to work with fonts (not just embedded fonts but also to set sizes and other styles) and they are included in the PDF specification (https://www.adobe.com/content/dam/acom/en/devnet/pdf/pdfs/pdf_reference_archives/PDFReference.pdf), for example:
BT% Begin text object
/F1 1 Tf% Set text font and size64
0 0 64 7.1771 2.4414 Tm% Set text matrix
Maybe the service you are using requires using PDF/A-2b (ISO 19005)? Although we recommend you to contact them to know why that service doesn't accept PDF documents that use F* elements that are included in the PDF specification. If you are using the conversion plugin based on LibreOffice you could try generating a PDF manually testing the included options in the Export dialog (PDF/A-2b, Tagged, XObjects...) to check if enabling any that service accepts the PDF.
Regards.