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First, I sincerely hope you have a couple of backups of these images. SD cards can suffer from bit-rot (especially when hot), file system corruption, physical failure, and loss. Heavily-used cards are especially prone to problems. All is takes in one unexpected battery depletion whilst saving or manipulating the files and the file system becomes corrupted. Worse, corruption can be invisible such that you may not realize the newly saved images are over-writing parts of all your older "most important" shots.
Instead of keeping all your most precision eggs in your most heavily-used basket, you might want to split the task -- use one card for archival storage (with backups!) and a second card for active shooting.
That said: If your still want to keep a zillion JPEGs on the card but not have them load, you might try partitioning the card (which requires erasing the card), seeing if moving the old images to a strangely-named or placed folder help hide all those files from the app's default behavior. For example, the app might only look for images in the DCIM folder so a second root-level folder named whatever might not be subject to the slow thumbnail loading process. Or perhaps you can rename all the .JPG files to .PJG but then configure your PC and your phone to associate .PJG files with your image-processing software.
Final Caution: The people who write all software for your camera, the FlashAIr, your phone, and your PC all assume you've done nothing strange -- that the card contains standard image files, stored in the standard way, in the standard places. Any non-standard tricks you do to hide files or speed the handling could have unexpected consequences because you've done something that no one thought you might do.
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