Game freezes up every few seconds. I don't have any regular radars and I was using VisionRadar so I thought maybe that was the issue so I removed it but it still happens. I doesn't appear to go away with time.

The game will freeze while the map is processed and it can take several seconds for hidden edge chucks to regenerate. I suspect that this may be an interaction with another mod. Could you post your mod list from when you first noticed the behavior?

OK, I'll let the save run for some time and report back. I don't see any output in the console. It was working fine in .17 but I also was able to run the game at double the speed and now I'm struggling to run 50 ups as I'm approaching stable 2700 spm.
https://imgur.com/l4LuAQN

I doubt the issue is with Delete Empty Chunks. There is no active on_tick elements. Everything is a one-shot function when the button is pressed.

I've been playing my pre delete chunks save for a few days. I opened a save from right after I ran it and it still freezing up. The interval does seem to reduce after a few minutes but it's still freezes up every 10 or so.

Can you post an image of the debug info with "show-lua-object-statistics" active from when it is freezing?

https://www.youtube.com/watch?v=rzSyF0QNubo&feature=youtu.be
Edit: Made the video public. Also, this is right after I clicked the delete chunks for the first time

So watching the output, you can see that, just as the game unfreezes, mod-rso-mod is taking upwards of 2157ms (over two seconds) to update. I don't use RSO myself however I did install it to verify that it still works as expected. It is possible that on your map with almost 970 hours of play time may have some accumulated data that RSO becomes unhappy after 48,532 of the 58,836 chunks on your map get deleted. I am unable to recreate the issue on my end with a trivial map. Unfortunately this looks like an RSO issue. If there is something I could do on my end to make them play nicer together I would.

Thank you! Uninstalled RSO and deleted chucks with no freezes and I'm almost at 60 ups. I'm at the point where I don't really need new ore patches anyway. That output awful lol. There should be a checkbox to show the worst mods sorted by UPS usages and have it sample over a few seconds so it doesn't resort too much. Maybe a "Bad Mod" mod haha.