It seems with a lot of alternate cryptocurrencies that forks are a serious problem. Due to attacks or multi-coin pools throwing insane amounts of hash power I have noticed a few of my coins regularly show issues with blockchain download giving error: Warning: Invalid checkpoint found! Displayed transactions may not be correct! you may need to upgrade, or notify developers.
I have found someone who has had a similar issue here: https://cryptocointalk.com/topic/7060-ann-fluttercoin-flt-pow-pos-and-new-proof-of-block-pob-mining/page-2
However, they are told to delete the blockchain and start the client again. Due to the already gigantic size of some coins (especially coins with low targets and thus high block generation rate) which is growing, I am less and less inclined to use a shortcut such as this, especially since I feel this creates a weakness in the network if a large portion of users have this problem, and all delete and restart their blockchain. Not to mention larger coins such as copperbars takes approximately 2 days being the only daemon to catch up on my desktop.
Is there anything I can do to help prevent these issues, and if I do get these kinds of issues, is there anything I can do besides "delete everything and start over"?