Hi Ashok
I use LR Classic which is slightly different I think but my suggestion would be: if you still have the file(s) on the SD card, delete the version in LR and then re-copy them from the SD card to LR using LR Import.
Or, If you know where the image is on your external HD, you can, as you have seen, point LR to it and LR will then change the location of the picture on its database. I think you could batch move these by going into the grid view, selecting the images, right clicking and then Go To Folder which will show their location in LR. You can then drag them where you want. Obviously though if they are in different folders to stat with, batch moving may not be feasible. What you don't want to do is move their location outside of LR. LR then gets lost.
I'm not sure if that helps or not!