Hi!
The comments, if not saved with an ID, will only be populated and saved on the SOP document they were entered. This is true for header level comments as well. There is no function that I am aware of where GP removes these from the system without user interaction.
If you run the Sales Line Items Smart List report with the line comments as a field, you should be able to see all the lines of a SOP document for whatever search criteria you need. I would run this for your orders entered in a specific time frame to see if this is a one-time issue, or if this is affecting other documents as well.
You should also note that once the SOP document is posted / transferred, you cannot change these without modifying SQL.