Hello Richard,
I'm sure you know, but I'll put here anyway.
You can't get the FK to be included automatically in the excel.
The platform won't recognize them even if the data in the excel has the same underlying data type as the Entity Identifier.
The solution is:
1. Add the IDs to the excel
2. Do the bootstrap normally, ignoring the platform will not have a match
3. In the structure created by the automatic bootstrap, add the two fields that are missing. But add them as Integers instead of Entity Identifiers. Also, be sure the newly added attributes are in the same order as the columns in the excel, or you may get an error.
4. In the Bootstrap, select the Assignment node and add manually the missing two fields, making the conversion from integer to identifier (if they are integers), or from text to identifier (if they are text).
I did this many times in the past (and just tested it) and this works.
Cheers