Hi Jen,

We're looking into the performance issue you've described. In the meantime, have you looked into our study archive format and automated reload functionality? This was designed to handle exactly the scenario you're describing by allowing new and modified dataset and specimen data to be merged into an existing study:
https://www.labkey.org/wiki/home/Documentation/page.view?name=importExportStudy

If this path looks like it could work, the easiest way to proceed is to export your study using the new XML formats. This file will be used as a template for your nightly reload. After unzipping the file, all you need to do is replace the data for the modified dataset(s) import the data back into the same study.

Let us know if you run into trouble.

Thanks,
Britt