So, interestingly the two old chains were issued minutes after the two new chains. To the best of my knowledge, all four chains should have been the same chain structure based on the update timings. Unfortunately, I could find no history on crt.sh to know which certificates were sent by Boulder during the issuance process as there was no apparent indication which version of the R3 intermediate (signed by DST Root CA X3 or ISRG Root X1) was used to sign the certificates. The situation is very peculiar indeed as there is no logical reason that Boulder would be issuing the new chain and then somehow revert to issuing the old chain minutes later without some time of temporary fallback occurring (unless there were multiple Let's Encrypt servers operating under a rolling restart and your later certificates somehow were issued by unrestarted servers while the earlier certificates were issued by restated servers).