? in cram files

I have an original bam file that when compressed to cram format, the quality encoding scores are lost and replaced as question marks ? and other symbols. The following questions come up:

1. Why is it that the original base quality scores are changed when
   compressing from bam to cram?
   1. Is it possible to map back the base
      quality scores from a cram file to original bam file using a
      reference file? Or a tools such as BaseRecalibration from the GATK
      package?

Example:

Converted Cram File

CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAACCTTACCATAAACCTAACCCTAACCCAAAACCTAACCCATAAACAAACCATAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

????????????????????????????????????????????+5?++5?55????+??++?5??’+??’+’+?+++++??’?5++++’+++&+?5+++’++++++’++’++++++++++?+++++????+???+?????+?????+???

Original Bam File

CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAACCTTACCATAAACCTAACCCTAACCCAAAACCTAACCCATAAACAAACCATAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE,5E,,5E55EEEE,EE,,E5EE;,EE;,;,E,,,,,EE;E5,,,,;,,,&,E5,,,;,,,,,,;,,;,,,,,,,,,,E,,,,,EEEE,EEE,EEEEE,EEEEE,EEE