Basically, your plan is sound. It just depends on how long you want to keep the details (individual versions) of items during these few weeks.
Yes, by all means simply create an archive and schedule it to capture just the activity of your working folder(s) for the short term.
When you have access to your original archive again, it will resume capturing your documents. Afterwards, your original archive will have the latest backups, it will just be missing the intermediate versions of the past few weeks.
If you're anxious to maintain those intermediate versions, simply hang onto the temporary archive for awhile.
There's no direct way to directly inject the history of one archive into another archive. It would be possible to script this using the command line tool—the script could run in a loop recalling each layer from the temporary archive and then capturing that into the original archive. The layer dates would be off, but it would replicate the sequence of versions in your original archive. It also seems like an excessive amount of work.