Replace symbolic-link with target

Here are versions of chmeee's answer that uses readlink and will work properly if there are spaces in any filename:

New filename equals old link name:

find . -type l | while read -r link
do 
    target=$(readlink "$link")
    if [ -e "$target" ]
    then
        rm "$link" && cp "$target" "$link" || echo "ERROR: Unable to change $link to $target"
    else
        # remove the ": # " from the following line to enable the error message
        : # echo "ERROR: Broken symlink"
    fi
done

New filename equals target name:

find . -type l | while read -r link
do
    target=$(readlink "$link")
    # using readlink here along with the extra test in the if prevents
    # attempts to copy files on top of themselves
    new=$(readlink -f "$(dirname "$link")/$(basename "$target")")
    if [ -e "$target" -a "$new" != "$target" ]
    then
        rm "$link" && cp "$target" "$new" || echo "ERROR: Unable to change $link to $new"
    else
        # remove the ": # " from the following line to enable the error message
        : # echo "ERROR: Broken symlink or destination file already exists"
    fi
done

You didn't say what names the files should have after the replacement.

This script considers the replaced links should have the same names they had as links.

for link in `find . -type l`
do 
  target=`\ls -ld $link | sed 's/^.* -> \(.*\)/\1/'`
  test -e "$target" && (rm "$link"; cp "$target" "$link")
done

If you want the files to have the same name as the target, this should do.

for link in `find . -type l`
do
  target=`\ls -ld $link | sed 's/^.* -> \(.*\)/\1/'`
  test -e "$target" && (rm $link; cp "$target" `dirname "$link"`/`basename "$target"`)
done

If you are using mac OSX aliases, then find . -type l won't come up with anything.

You can use the following [Node.js] script to move/copy the targets of your symlinks to another directory:

fs = require('fs')
path = require('path')

sourcePath = 'the path that contains the symlinks'
targetPath = 'the path that contains the targets'
outPath = 'the path that you want the targets to be moved to'

fs.readdir sourcePath, (err,sourceFiles) ->
    throw err if err

    fs.readdir targetPath, (err,targetFiles) ->
        throw err if err

        for sourceFile in sourceFiles
            if sourceFile in targetFiles
                targetFilePath = path.join(targetPath,sourceFile)
                outFilePath = path.join(outPath,sourceFile)

                console.log """
                    Moving: #{targetFilePath}
                        to: #{outFilePath}
                    """
                fs.renameSync(targetFilePath,outFilePath)

                # if you don't want them oved, you can use fs.cpSync instead