If the problem really is just stale metadata, then you can fix it simply by running reload indexes to flush the metadata before you run the install.

The more likely explanation however, is that the machine you built the autobundle on was not running the latest version of those modules. When you use autobundle to create a bundle, the bundle includes version information for all the modules that versions could be determined from. When you try to install the bundle, it will try to match these version numbers. Since the intent is for an autobundle to be able to exactly replicate the environment from one machine to another, it makes sense to match the version nubmers. On the other hand, minicpan just gets the latest version of each module, which leads to this problem.

The easiest way around this is to remove the version information from the autobundle before trying to install it.