awk -v m=50 '
  NR==FNR {                         # For each line in the 1st input file (file2)...
    for(i=4; i<=NF; i++) {          # for all ranges in $4 and further
      split($i,F,/-/)               # split the range in a left field and a right field
      L[$2,i-3]=F[1]                # Assign them to multi-dimensional associative array L(eft)
      R[$2,i-3]=F[2]                # And R(ight), which will be needed in the second part
      N[$2]=NF-3                    # Record the number of ranges in associative array N for index $2 
    }
  } 

  $9=="." && $12=="." {             # For each line in the 2nd input file (file1) if both field 9 and 12 equal "."
    d=">50"                         # set the default difference to >50
    for(i=1; i<=N[$8]; i++) {       # loop over the number of ranges for key $8
      if((d1=$4-L[$8,i])<0)         # set the left difference for a range
        d1=-d1 
      if((d2=$4-R[$8,i])<0)         # set the right difference for a range
        d2=-d2 
      if(d1<=50 || d2<=50) {        # if either of those difference is less than or equal to 50 
        if(d1<=50 && d2<=50) {      # if they are both less than or equal to 50
          if(d1<d2)                 # calculated the smallest difference. 
            d=-d1                   # If it is the left one then the difference is minus that value
          else                      #
            d=d2                    # If it is the right one then the difference is plus that value
        }
        else {                      # if only one of them is less than or equal to 50
          if(d1<=50)                # if it is the left one
            d=-d1
          else                      # if it is the right one
            d=d2
        }
        break                       # found a match, no need to loop further (assuming there are no overlapping ranges) 
      }
    }
    $9=d                            # set field 9 to the difference that was found
  }
  1                                 # print the record    
' file2 FS='\t' OFS='\t' file1