From what I've read, it might depend on the version of TWRP you're using. Here's a link to another user's experiences using the OTA updater with different TWRP versions...
The updater app has had issues on the OnePlus 3/t for quite a while. It's safer to update by downloading the zip from the LineageOS website directly, booting into TWRP, and flashing it yourself from there. :)