Photocopy them - Scan to paper
Since you're keeping the receipts as paper, I'd photocopy them or scan them to paper (many receipts to a page) and store them with that month's receipts. Depending on how many receipts you're tracking, I'd only bother to do this for receipts that were not paid by check - in other words those that were paid by petty cash. I'd only do it with the receipts that are on the paper that fade. I might also do it with one's that fade that get charged back to multiple accounts - a receipt that includes office expenses, cleaning supplies, supplies for repairs, and personal expenses. You know, a trip to Sam's, Costco or BJ's. :-0
If you're not going to be processing these right away - try to separate them by month when you're stuffing them in the "shoebox" to process later. I did the paperwork for my husband's business for 20 years. I got him to circle the date, write the check number and amount paid (which didn't always match the invoice amount when there were also sheets of returns included). He also would put petty cash receipts in an envelope for each month and at the end of the month file that with the months receipts. His business wrote about 100 checks monthly, including payroll and probably had about 30-50 petty cash receipts.