scATAC-scRNA integration, change to pair cells

[TauHHCC]

Or, follow my last question #1959.

If I reorder after the integration. I mean take the integrated arch project, check cell name and its assigned scRNA cells (integration@cellColData$scRNA$orig.ident). If their names are not paired, find the paired one and reorder it.
It seems not very difficult to make a new order in integration@cellColData$scRNA$orig.ident.
Should I also reorder the following RNA information? Or the data structure is it finds its assigned scRNA cell, and then went to GeneIntegrationMatrix to search this cell's RNA information, thus I just need to make new order in that column?
Another wired thing is, I couldn't find GeneIntegrationMatrix in the integrated project using getAvailableMatrices(integration).
Best.