When building indices in CirrusSearch we create a new index, for example enwiki_content_1234567. The final step of building this index is to change the enwiki_content alias to point from its current location to the new index, and delete the old index. To support building indices that contain multiple projects we will need to run the build process on multiple independent wiki's and finally promote that new index by assigning the alias to it after all projects have finished the build. Adjust maintenance scripts to make this possible.
Note that how this works depends on the process being done. Updating the mapping for a wiki is generally done by reading out the current index state and writing it to a new index. In this case the process can still be "one and done" rather than distributed across multiple projects.