theres an easier way...somewhere in options its like move track automation to region or vice versa, then you can have a midi region with automation that u can loop or whatever. havent been on logic for a while but its definitely there found it really useful once u get used to it aswell
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just re-read your post, theres a 'mix' setting on autofilter isnt there? either that or dry/wet. you should be able to automate it from 0% to 100%(or whatever %) on the last bar.
ACTUALLY, on autofilter i think its best to automate the cutoff mod. for the lfo (or envelope) at 0% the filter should do nothing then u can automate it to what u want for the last bar.
sorry if this isnt the problem u have