I have 3.5" EXT4-formatted HD in an externally-powered USB enclosure attached to a Pi 3B+ running the latest Raspian Stretch Lite. If I flash a new SD card, I'll see a sustained large-file transfer rate of over 35MB/sec (280 Mbit/sec) to/from the hard drive.But after some hours or days, the best-case transfer rate suddenly drops by about 20%, and the most I can ever achieve is less than 30MB/sec. This is with nothing changing on the hard drive itself, and it doesn't seem to be related to temperature, reboots, or any other software packages being installed. Nothing I try restores the transfer rate, except for reflashing the SD card - if I do that, I immediately see the higher transfer rate.
I'm using a 3A power supply and I don't believe I have any power or temp issues. vcgencmd get_throttled always shows zero. Rebooting will not restore the higher transfer rate. In all cases, iperf3 shows a very consistent 280 Mbit/sec transfer rate over gigabit ethernet.
It's almost like something trips, and it permanently throttles the disk throughput from that point forward. Can anybody explain what could be going on?