While what you see is a bit unusual, it's not a total surprise since the text engines change from version to version and going backward requires the text to recompose with the older engine. Without seeing the actual file it's pretty hard to say exactly what's going on, though. Do the frames show overset when first opened?
I'm trying to open the idml file again and make a screen shot. It just crashed InDesign 6. Will keep trying to open it.
The frames do show overset when first opened. I was able to open it after the crash.
@fradcar – I can see something like this sometimes when opening an IDML file. But it's only for a brief moment, then the text frames are redrawn, the document is recomposed and the text is showing up. However, I can remember very rare cases where showing overset text frames remain in an overset state.
As you already found out, changing the width or height of a text frame will force a recomposition and the overset state will vanish. I guess in your case changing back the width to the original value will not force overset in this fassion (only, if a new line is added, because of changed line length due to a different text engine).
Without having direct access to the IDML file, I cannot say, if it will help "shaking" the text frames by script.
I set the amount of changing the width and height of each text container of every story in the active document to 1. You can change this in line 7 of the code, if you like.
How to install and use scripts: