So if I interpret correctly...
1. Newlaptop files ----> external HD, then
2. Oldlaptop files ----> external HD
3. after #2, files from #1 no longer found on harddrive
That should not be the case normally, unless you copied FolderA from Newlaptop, then copied FolderA from Oldlaptop, causing FolderA to replace FolderA...you overwrote the exact same name folder (or individual files) from two plcase, causing one to overwrite the other.
If, after copying files from LaptopA to HD, you 'erased' the files from LaptopA, if you did not yet 'Empty Recycle Bin', you can recover the deleted files/folder in LaptopA back to their original folder locations. Simply Left Click on the Recycle Bin desktop icon to open it, then select the file(s) and Right Click and choose 'Restore' from the menu that pops up.