Welcome to the forum.
In theory, you can use the FilterObjects module, select the filtering mode and method to Measurements and Limits then the option for filtering by Parent/Child should come up, where you can set a minimum meaurement value to be 1.
However, from your post it sounds like you have changed the example pipeline compared to what I just downloaded from the website. For example, when you discuss secondary objects I assume you using the IdentifySecondaryObjects module which doesn’t appear in the example pipeline.
The reason I am asking is because if you are using the IdentifySecondaryObjects module I believe my suggestion above won’t work as that module uses every primary object there is to create a secondary object so the ratio should always be one to one.
If will work however if you are using two IdentifyPrimaryObjects modules and then using the MaskObject module as in the example pipeline is (for future reference, the RelateObjects module is another way to do this that might work) then filter objects should work fine.
Sorry, if that’s a lot of confusing information. If you need more help then you could maybe upload the pipeline you are currently working on and an example image set.