# If you'd like to omit non-matching lines from the result; add ';d' to the end of the expression.
sed -E 's/(\d)(,)(\d{3})(?=(?=.*?:).*?~.*?;0*\1\3_(.)(.{3}))|(\d)(,)(\d{3})(?=.*?:)|(\d)(:)|(#),/$2$7$4$6$5$8$10$9$11/g;t' <<< "#,0001,0110,0010:~;0101_1000;0110_1001;0111_1010;1000_1011;1001_1100;1010_1101;1011_1110;1100_1111,~0_00001_00012_00103_00114_01005_01016_01107_01118_10009_1001,"
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for SED, please visit: https://www.gnu.org/software/sed/manual/html_node/The-_0022s_0022-Command.html