Okay, sounds like you could use a simplified version of Pieters method:
To get an array of all records that exist in both tables:
Use intersection(variables('BigArray'),variables('SmallArray')) and store it in a variable, lets call it CommonRecords
Then use a filter array action, where you filter the big array, and as the filter condition use:
contains(variables('CommonRecords'),item()) is equal to false
The output of this will be an array which holds all the records from the big array which are not present in the small array