I'm having the same problem as you. Sorry, not being very helpful, I know, but hopefully someone else will!
So I never worried about FTP until I purchased the TACX Neo 2T. Now I know my FTP is 235. On December 25th Garmin Connect shows my ride power curves correctly, with a 20 min value of 231 - but on that same day it shows my FTP as 320? How/where/why did it get that from? I went in and updated all my devices with manual FTP of 235. Ensured they were synced. Retired old devices I wasn't using anymore just in case. Ensured the auto FTP was switched off on my devices. Updated manual FTP again on all devices. Synced again. It still says my FTP is 320!!! I have a Garmin scale too. My weight is correctly being input to calculate my watts per KG - but using 320 W instead of 235. Common Garmin!
I've spent thousands on the NEO2T, Forerunner 935, Garmin 820, Garmin Scale, Garmin Bluetooth HR Strap. Literally - all my devices are Garmin so there shouldn't be any vendor incompatibility issues. Seriously my time is valuable and I shouldn't have to spend literally hours trying to troubleshoot this!!!
I'm in exactly the same boat with a Neo trainer and Edge 1030, FTP values all correct on the Edge and in Garmin Connect web and mobile app yet it calculates IF based on a FTP of 500 when it should be 250. I've ensured my recording is every second and including zeros as suggested by many forum threads yet Garmin continues to underestimate my IF by half while it shows up correctly on both Rouvy and TrainingPeaks. This seems to be an ongoing issue and despite talking with a Garmin rep today for 45 mins telling me to do all the things I was already doing it did not get resolved. Frustrating to have to spend this time figuring out problems that shouldn't exist! Please fix already Garmin!!!!!!
Make sure Auto Detection is turned off for FTP.