I also tried this. On one wallet it worked, but on another it hasn't. I even went so far as to transfer all the coins out of the wallet, completely deleted the wallet.dat and blockchain (everything in the data folder) and let the blockchain download from scratch. Still have that checkpoint message.
It doesn't hurt anything though, right? I'm still solo mining fine.
It shouldn't hurt anything as long as you are on the correct chain but while you are seeing that message there is no way to ensure that.
If you have a client that has synced correctly, try following these directions to get them both working right..
0. check you disks for corruptions, chkdsk or something similar
1. stop both clients
2. make a backup of the wallet and the chain on the broken client (wallet.dat, blkindex.dat, blk0001.dat and database folder)
3. delete the original blkindex.dat, blk0001.dat and database folder in the data directory of the broken client
4. copy the .dat files and database folder from the working client computers data directory to the broken clients data directory
5. open a command prompt or shell
6. run "starcoin-qt -rescan"
7. once the client opens, open the debug rpc console
8. if your wallet is locked unlock it using walletpassphrase 99 false
9. run the command checkwallet
10. if checkwallet found problems run repairwallet
11. you should have working client with your previous balance restored
12. if you wallet hasn't locked itself you can re-lock it with walletlock
Hope this helps,
ps. as a general rule it pays to keep a copy of the blockchain handy in case you need to restore it due to a corruption, saves having to resync the whole thing, eventually I'm hoping to provide a downloadable copy of the blockchain to save time resyncing

infin.