When your script is opening files, you are using the Open method with a set of open parameters. There are various parameters that tell FrameMaker not to resolve references, not to complain about missing fonts etc. You shoud make sure all those options are set such that nothing can stop your process. Use the FDK Reference Guide - look for GetOpenDefaultParams( ) - to find the full list. I have copied the ones that may cause unwanted blocking messages. I am just naming the param ident names and the values to set. You know how to handle an array of PropVals (otherwise you would not have your script open files at all).
FS_FileIsOldVersion -> FV_DoOK
FS_FontChangedMetric -> FV_DoOK
FS_FontNotFoundInCatalog -> FV_DoOK
FS_FontNotFoundInDoc -> FV_DoOK
FS_LanguageNotAvailable -> FV_DoOK
FS_LockCantBeReset -> FV_DoOK
FS_RefFileNotFound -> FV_AllowAllFilesUnFindable
FS_UpdateXRefs -> FV_DoNo (this could make your process a LOT faster, and I am guessing your XRefs will either have to be re-created or updated by your script, or remain as they are).
I hope this helps.