A common way to deal with this is called an escape character or qualifier. Consider this Comma-Separated line:
Name,City,State
John Doe, Jr.,Anytown,CA
Because the name field contains a comma, it of course gets split improperly and so on.
If you enclose each data value by qualifiers, the parser knows when to ignore the delimiter, as in this example:
Name,City,State
"John Doe, Jr.",Anytown,CA
Qualifiers can be optional, used only on data fields that need it. Many implementations will use qualifiers on every field, needed or not.
You may want to implement something similar for your data encoding.