Yes.

Search for the keyword "Lane Initialization and Reversal" in the user guide at the URL link below and refer to it.

https://www.altera.com/en_US/pdfs/literature/ug/ug_pci_express.pdf

Table 9-5.Lane Assignments with Reversal is the replacement pattern.
for example
- Core Config : 4
- Slot Size : 4
, the 2:1 (swap lane2 and lane1) and 3:0 (swap lane3 and lane0) swaps are automatically recognized.