A bad or corrupt upload will result in a 'CLON NG' display message. A flashing programmed channel display usually indicates something more sinister.
Unlike other /\/\anufacturers, selecting 'New' in Icom cloning software always generates a clean and correct .icf file. Opening the software and cloning in a simple one-freq file with no other changes will create a valid .icf and clone. There is NO 'codeplug' as such - that is a /\/\other term.
The exception is when Maker Reserve mode is running. In that case the cloning software will upload radio-specific alignment data along with the channel and feature data. As I recall (remember it's Sunday morning before coffee #2) cloning software always downloads all data, but only uploads radio specific alignment data when M-R is active. If you create a new .icf with M-R running and upload you will wack the radio. Icom does cloning in the reverse manner from others - .icf files may be freely cloned between same model/firmware radios (with M-R off) and cloning only uploads the channel and feature data (not alignment data) by default.
Hence, the reason Maker Reserve is difficult to get into and dangerous to run if you don't have a specific reason to go there. If you don't know how to get there you are on your own.
While it may provide a starting point for alignment, such data is not interchangeable between radios. A M-R active clone from a known good .icf file may give you a starting point, but you will need to break out the service monitor, signal generator and the rest of the toys and perform a full alignment to get things back to normal. Accurate alignment is impossible to do without them.
PS: Always read and save an .icf before making any changes. My server has almost 2 Gig's of .icf files going back almost ten years and it has saved my bacon more than once.