I apologize if I'm not understanding correctly, but I believe you can set a filter to be "on by default" in both the web map and the web app. I have a map/app with a data set of over 200,000 parcels, and I applied a filter in the web map so that only around 37,000 of them display when the map/app is opened. This was essential for us so that the layer would actually draw! I didn't notice any lag associated with panning/zooming or searching, so I'm not sure if my situation is different.
The only other option I can think of is to use the Extract Data tool (under "Manage Data") within the Web Map through the Analysis ribbon. But sounds like that might not be ideal for you?
Sorry, I can't be more help, maybe someone else might have a better idea! Best of luck!
Best,
Katie
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