I am not sure I can answer your question without context except through an educated guess. What species are your working with ? The subseq coordinates in the gff file should ideally have been assigned as an offset from the start of the sequence file to where they are regardless of their chromosomal position. Another possibility is that the gff files for each chromosome have been generated individually. In the first case using the coordinates can get you the region corresponding to the chromosome without needing to worry about chromosomal location. In the second scenario extracting the subsequence will be as simple as accessing the right chromosomal gff file.