From the design:

Update and delete are both write commands which are handled through the BatchedCommandRequest class. The "q" field on UpdateOpEntry and DeleteOpEntry contains the BSON for a MatchExpression. If there may be FLE2 rewrites to be done, after update and delete commands are parsed we will add a transformation pass similar to findAndModify which will take in BSON for a MatchExpression and return BSON for the rewritten MatchExpression, calling rewriteQueryOnEncryptedFields() on the parsed MatchExpression. This rewritten match expression will be inserted into the parsed request document and returned from the parsing functions.