Your encoded text is [B@6499375d
. That is not Base64, something went wrong while encoding. That decoding code looks good.
Use this code to convert the byte[] to a String before adding it to the URL:
String encodedEmailString = new String(encodedEmail, "UTF-8");
// ...
String confirmLink = "Complete your registration by clicking on following"
+ "\n<a href='" + confirmationURL + encodedEmailString + "'>link</a>";