Does it still happen when you have Clock Send and Receive Send turned off on the A4? I’m wondering if it’s sending a clock to Logic/Ableton/Etc and depending on what you’re using it rebroadcasts that clock signal back to the A4.
Not sure why it would only affect trig deletion though and not recording trigs as well, although it’s possible the trig deletion is slightly more difficult to calculate and takes just a bit longer for the CPU to compute which is just enough time for the multiple clock signals to confuse it.
I live in fear of midi loops, so anytime I want something to be just a slave I turn off all the other options it has to be a master, sometimes tracking that stuff down can be a nightmare.