Errr... your mods "Will" be uninstalled after you reinstall fallout 3, and only fallout 3. your BSA's should be in Fallout 3 / Data folder and no where else, also, you "must" install fallout 3 completely, not just uninstall it (if you didn't really mean reinstall :D), then the BSA files are there, trust me, if you don't see them, with all said above, then you have a serious problem and you "must" contact sheogorath. I made new mods after reinstalling. Do you know how to change the folder where your made mods with geck are places after saving?