I encounter this bug quite often in many different occasions. When I copy/delete/pack/unpack something it is seen in Explorer quite good, but MC doesn't see it for a long time. Typically Refresh button helps but not in all cases. You should do something with responsiveness to events in filesystem.
Example: I overwritten the big iso file (which was 3.5Gb and became 3.9Gb). It was recognized in Explorer immediately but in MC - never. On the screenshot the same file is opened simultaneously in Explorer and in MC.
I waited for a long time but without success, maybe after 10 minutes file list was refreshed, I didn't check up.
It is considering that fact that copy/overwrite operation was done via MC, not via Explorer. It is quite shame to observe such slowpokeness.
I can give dozens of such examples, I observe this quite often.