Why do you have them all as jpeg?
What was the original format? Why not leave them as the original?
Or save all the files as hi-res Jpegs and place those.
There's no need to have 2 jpegs of the same image (one small and one large) use the highest res image for both - indesign does the rest when exporting pdf.
Be assured, that when placing an image in Indesign it does not lose any resolution at all. From your description I read that you refer to the PPI as resolution, not the dimension in pixels.
Only when exporting them to PDF you define the export resolution plus a quality level. Both can significantly reduce the visible impression of an image.
. I was looking at the effective PPI and the original PPI, and indeed those images that loose resolution jevae a lower effective then original.
If the effective res is lower than the actual res you must have scaled the image on the page. In design resizes images when you scale-- there's no resampling. So a 300 ppi image scaled to 200% becomes 150ppi, the pixels double in size.