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Before going into the portal (whenever you decide to do that), press the Select Tool,
Select ALL your nodes,
Click Save and you'll get a stacked Schematic with a ton of nodes
Load that Schematic
and bam, you'll have a metric ton of nodes and you should get the achievement. If you didn't, then load it again.
Then enter the portal to avoid having to worry about cleaning up.
The research center itself has a speed at which it processes whatever files you input and upgrading it improves that speed. Overall, as long as your research node is keeping up just fine, it's better to use a file type you're producing more consistently.