Handling sample identity in aggregated 10x libraries? cellranger aggr can combine multiple libraries (samples), and appends each barcode with an integer (e.g. AGACCATTGAGACTTA-1). The sample identity is not recorded in the combined matrix.mtx file.

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/aggregate#gem_groups

How can we keep and assign sample information to each cell after loading the data into R? (e.g. Seurat::Read10X())
You have to keep track of the file order you used for aggr.  The suffix number represents which represents the aggregated sample. You could store this information in a text file and load it into R independently of the Read10X function and combine it with the cell names to get their sample names. From the page you link:


  Gem Groups
  
  This is an integer that is appended to each barcode in the
  gene-barcode matrix. For example, AGACCATTGAGACTTA-1 and
  AGACCATTGAGACTTA-2 are distinct cell barcodes from different
  libraries, despite having the same nucleotide sequence.
  
  The numbering of the GEM groups will reflect the order that the
  libraries were provided in the Aggregation CSV.