Are you putting two or three sets of nutritionals on, i.e. is this per 100g, per pack and per portion, or is one pack the same as one portion?
If your pack size is x grams and you're defining your portion size as x grams then surely this isn't a problem?
In any case, the nutritional values themselves will also almost certainly be subject to natural variation (unless you're packing something that is genuinely fully standardised), and this is acknowledged by the current regs - you may already be familiar with the guidance on it but if not then this link is worth a read: https://ec.europa.eu...ces_1212_en.pdf
As long as your pack quantities comply with Weights & Measures regs then I genuinely don't think it would be at all concerning for regulators even if you were saying "per pack" rather than (or as well as) "per portion", as the actual variation this is likely to cause is still potentially smaller than the inherent natural variation in many products. We've had various labels with "per bottle" in addition to per 100ml data checked over by Leatherhead and Trading Standards over the years, the latter directly following a discussion about the type of average fill controls in operation, and the question on per pack nutrition has never come up.
If you wanted to be extremely thorough you could do some quick calculations to reassure yourself - i.e. assuming your current nutrient values per 100g are "right", what is the effect on the values per pack for each nutrient based on pack size at both the top and bottom ends of the average fill weights, and how does this compare with the tolerances per 100g permitted in the guidance when translated into a tolerance per pack based on your pack size?