I'm still fairly new to Canvas Data myself, but I'm going to try to answer this if only to help collect my own understanding.
The /file/sync endpoint and algorithm specifically refer to the TSV files that exist in the Canvas Data platform. The sync list contains all files that are needed for a complete snapshot of data. The last step is to delete any files previously downloaded that is not in the current sync list because all that data now exists within a new file.
The new file will need to be ingested into your data lake to insert new rows and update existing rows. Since comparing each row can be expensive, it may be simpler to truncate the table and reload it with the new file(s).
You my also see files in the sync list that you have already downloaded. This indicates that the data within that file is unchanged, but are still needed to get a complete snapshot of the data
If you are truncating your tables you will need to reload these files to get the complete set of data. However, if you are comparing rows you may be able to skip these files entirely because nothing has changed.
You will not need to keep or ingest any files that are not in the current sync list, unless you want to keep some sort of change log of the data over time.