Is there such a thing as a legitimate retroactive plan document amendment (not going through EPCRS, but conforming the plan to actual procedures). E.g., if you have a corporate resolution specifcially merging two prototype standardized plans, but the plan document amendment was never signed (even though the adoption agreement is accurate because it was based on the expiration of the 410(b)(6)© period - particpants in plan two will participate in plan 1 as of end of 410(b)(6)© period). I know it's a long shot, but I thought I would ask.

No, but you could argue a collection of documents if audited. You may or may not win. If you do win, it may be through court, not through audit CAP. See Engineered Timber Sales, Inc v. Commissioner.