If I'm understanding correctly, two possible answers might work:
1. Concatenate the 2 factors you are studying, and create a table where only valid L1 and L2 combinations exist. Use this new concatenated row as one single factor in your DOE with x levels, where x is the number of valid combinations.
2. Do the same as option 1 above, but instead of using this third/new column as a single factor, use the table with the 2 columns of valid combinations as covariate factors in the custom designer, making sure to specify to include all selected rows.
Example below of option 2, with 2 factors, with 3 levels each. I used the Full Factorial designer to create the table with factors/levels, then manually created/exclude the disallowed combinations. The exclusion portion of the work could likely be scripted.
Jed_Campbell_0-1669839818959.png