Lucee 6.1 seems to have a significantly different limit on function / file sizes, is this just an issue inherited by various updates that I should just deal with, or a bug ?

How so? What limits are you facing now that you didn't before?

we have an internal javascript module end point, written in CF... and yeah, I get it, it could be done better, but its 2000 lines, but the Lucee compile we run works fine on Lucee 6.0 and lower, but not on 6.1.

I don't have an answer sorry... In a roundabout way I was getting you to add more details - because without any context - you're question might not be immediately apparent. Although - while I am typing this - I think I remember a previous message - possibly here or in the Lucee forums - about the same thing....

Larger files with many functions have always been problematic with Lucee as often it creates a class per CFC instead of per function like ACF, but we've worked around this issue, how ever the limit appears to have reduced somewhat since 6.1 BETA