In the spirit of transparency, I have not worked with Eurofins data, nor can I find much on their webpage. Based on the description, I would use the out_table.biom and the OTU_representative_sequences.fasta as my starting place from their outputs. The tree tip problem has come up a few times, you might want to look at some of the threads I'll link at the bottom.
That said... if it were my data, I'd start over and denoise the data myself. You get higher resolution features and you know exactly how the data was processed bioinformatically.