Synchronising will detect the changes as additions and deletions (thus losing virtual copies, collection info, and possibly [if you haven't saved the data as XMP] metadata and develop settings).
If you've moved folders outside LR, you can use LR's "Locate missing folder" function (right-click on the red folder name) to re-link them and preserve all that data.
If you've moved files (e.g. merged several folders to be now a single folder) you can use the "Locate missing file" function (click on the question mark at the top right of the cell in the Library Grid view) to re-link files. LR's smart enough to check the new location for any other missing files at the same time: you don't necessarily have to locate each and every file.
However, if you've renamed files you will have to re-link each file manually.
Unfortunately, doing this from within LR is not straight-forward because since the destination folder is empty, it is not displayed in the library folder pane, hence I cannot simply drag the files.
If you select all the relevant files, then press the '+' next to "Folders" you get to create a new folder (OK, so it might already exist on the disk)
and optionally move all these files to the folder. You don't get a lot of flexibility in controlling where the new folder is made, but once it's made you can rename/move it within LR quite easily.