The .lnk shouldn't make them inoperable. The lnk stands for "link". Windows normally hides files extensions, but it doesn't matter if they are visible or not. The malware you had on your machine most likely changed the contents of the links which made it inoperable.
Right-click on one of them then select "properties" and see if it's pointed at the correct program. If it isn't, point it back to the correct program. You'll need to do this with every link that isn't working on yor desktop.