PIPS is another term for the small seeds found in fruits - such as grapes, citrus fruits (such as oranges, lemons, limes) and apples.
I honestly do not know how much pectin is contained in the seeds. I believe it would be minimal compared to the pectin in the fruit and especially the skin, pith and core.
Since many jam/preserves/marmalade recipes call for the addition of some lemon juice (for the acidity) I doubt that using lemon pips would adversly affect the flavor of your preserves.
I have made orange and lemon marmalades without the pips and they turned out just fine.
I would just stick to the recipe for whatever you are trying to make.