What is mamesl?
Sounds like some unofficial build which may produce a different output as the official one. Or it is a datfile which handles chd files differently.
There shouldn't be a problem with chds in official MAME .251 with or without software lists.
In general, if you place chds in a rompath root folder, the scanner (with all check/fix options enabled) detects wrong placed chds and moves them to their correct belonging (with subpath) path (don't allow chds on rompath root).
On the other hand, the all in one software list+mame mode isn't the best way to go since it's a pain to setup and usually takes way too long. Better use a single profiler per software list.
But of course, you can use the new rebuilder tool which is able to rebuild (or in that case move) chd files pretty quickly and supports MAME, MAME multi softwarelist and single software list mode out of the box.
Don‘t forget to name a concrete example which file was moved and how it was stored before. Best is to send over cmpro.ini, the settings cmp file for the used profile and the datfile (if no direct exe import) which was used. 4.047 had no relevant changes for the scanner at all.