It would help if you described these rc and sync files and showed us some of their content. From a quick glance at the manual, the script you refer to seems to summarize allele statistics from a raw dataset. If that's the case and you deleted all raw data, I'm not sure if you'll be able to go back in time and retrieve raw data from a summarized result.

.rc file looks like this

##chr   pos     rc      allele_count    allele_states   deletion_sum    snp_type        major_alleles(maa)      minor_alleles(mia)      maa_1   maa_2   maa_3   maa_4   maa_5   mia_1   mia_2   mia_3   mia_4   mia_5
 gi|42519920|ref|NC_002978.6     3530    A       2       A/G     0       pop     AAAAA   GGNNG   54/55   76/78   35/35   27/27   17/18   1/55    2/78    0/35    0/27    1/18
 gi|42519920|ref|NC_002978.6     5450    T       2       T/A     0       pop     TTTTT   ANANN   51/54   96/96   9/10    33/33   23/23   3/54    0/96    1/10    0/33    0/23

sync file looks like this

2R 2302 N 0:7:0:0:0:0 0:7:0:0:0:0
2R 2303 N 0:8:0:0:0:0 0:8:0:0:0:0
2R 2304 N 0:0:9:0:0:0 0:0:9:0:0:0
2R 2305 N 1:0:9:0:0:0 0:0:9:1:0:0

where

col1: reference contig
col2: position within the refernce contig
col3: reference character
col4: allele frequencies of population number 1
col5: allele frequencies of population number 2
coln: allele frequencies of population number n