How far back can you access your documents? Years ago, American Century lost my cost basis information for the "uncovered" shares of a mutual fund I have with them. So, whenever I sell anything from that fund, if it's an uncovered share, the tax statement shows its cost basis as zero, which then makes it look like the sale is pure profit.
I tend to be a hoarder, and in this case, it paid off, as I have just about every statement I ever got from American Century, even dating back to when they were 20th Century. So, come tax time, I give my income tax man the actual cost basis for those shares, and he uses that instead of the zero.
This has never raised any red flags with the IRS, but I do worry about it. So, whenever I sell off some of that fund, I always unload the uncovered shares first, in the hopes of eliminating any potential problems that might pop up, if the IRS ever questions it.
My guess is this wouldn't be a problem in a tax-deferred account like an IRA or 401k, where all of your withdrawals are subject to tax. But in my case, this particular account is after-tax.