One thing that helps me when my mSDs lock up on me or turn into super floppy is to do a full format back to default. I have a 128gb and it took me all day to do a full format. And that's on a cruddy netbook. Patience. I'm betting you don't have fakes. Formatting is a pain in the butt and is %90 of the problems.
First off, does windows even recognize the mSD cards? If so, open up partition master and see if the mbr has super floppy next to it. If so, one of the things I would have to do to on the blue button with diskwriter is first format it in diskwriter, then default format it in windows. Depending on the default (which is normally exFAT on large cards) I would first NTFS then use partition master to FAT32 it. It is important to do this because any FAT partition can easily become corrupted. So to clean the mbr properly you have to switch actual mbr formats.
I highly recommend using easeUS Partition Master to then FAT32 any mSD 64gb or above.
If windows doesn't recognize the mSD but does recognize the card reader, use a different card reader. Windows and card readers don't get along too well.
EaseUS must be Primary FAT32 and will default 32kb it. But to double check, run it under that other formatter I linked to and double check. You don't need to even format it. Just make sure the allocation size is right.
An occasional full (not quick) format can really help but takes a while. Also try not to move any files larger than 2gb on to the mSD.
I think the transfer limit is 2gb. I might be wrong. FAT32 has a file size limit for transfers. This might be what's making your roms go .bad on Sky3DS+. Hence the rom splitter tool from Gateway. Split 'em, transfer 'em, re-assemble them. Although, I think the limit might be 4gb, don't remember.
Yeah, it's 2gb. Just checked. Maybe try to trim the roms. This means get rid of the game manuals if you can. Try to make them 2gb or less. I know there's a great Sky3DS tool out there that trims better than any other program. Forget the name... where's fox? He should know. He wrote it. I loved it.
Sky Army Knife. It has a trimmer unlike any other. But some games are just too big. This means Gateway splitter.
Hope this helps.