OK, if I understand you correctly, the structure I should now have is /web containing the subdirectories /cops and /Calibre, with all the COPS files in /cops, and under /Calibre I now have only the subdirectory /Data containing my Calibre library.
When I type in
http://[IP]/checkconfig.php, I get a Synology splash page with the message, "Sorry, the page you are looking for is not found" and a "Back" button. I wasn't sure if you meant that or
http://[IP]/cops/checkconfig.php. If I try the latter, I get the error "HTTP Error 500 (Internal Server Error): An unexpected condition was encountered while the server was attempting to fulfill the request."
UPDATE: Doing some more Googling on this and similar 500 errors on Synology Diskstation, I found people mentioning that they had to enable an option "Enable display_errors to display PHP error message" in the PHP tab of Web services. Doubtless if weren't a total noob this would have occurred to me before. NOW if I do
http://[IP]/cops/checkconfig.php I get "Warning: require_once(config_default.php): failed to open stream: No such file or directory in /volume1/web/cops/config.php on line 9 Fatal error: require_once(): Failed opening required 'config_default.php' (include_path='.:/usr/syno/php/lib/php') in /volume1/web/cops/config.php on line 9"