Given that ConQat deals with COBOL badly, you might look at our CloneDR tool.
It has a version that works explicitly with IBM Enterprise COBOL, using a precise parser, and it handles all that sequence number nonsense correctly. (It will even read the COBOL code in its native ECBDIC, meaning a literal string containing an ASCII newline character doesn't break the parser).
[If your COBOL isn't IBM COBOL, this won't help you, but otherwise you won't "have to put a lot of hours to get anything"].
We think the AST-based detection technique detects better clones more accurately than ConQat's token-based detection. The site explains why in detail, and shows sample COBOL clones detected by CloneDR.
Specific to the OP who appears to be working in Japan: as a bonus, CloneDR handles Japanese character sets because it is implemented on top of an underlying tool infrastructure that is Unicode and Shift-JIS enabled. We haven't had a lot of experience with Japanese COBOL so there might be a remaining glitch; see G literals with Japanese characters.