Sorry, I've misread your original post. Now I see that you have 26k folders, not files. Well, reading and comparing 26k folders in 12 minutes does not seem that bad :) That's about 36 folders per second.

Log to comparison only - normal.
Need debug log ?

At comparison
CPU is 4-7%
ethernet (cable) about 150-200 kb/s send and 300 kb/s read
(speed is limited to 50Mbit/s per client at server)

It might be the comparison of 26K local files against 26K remote files that takes so long. Is CPU core maxed during the comparison? Can you post session log file?

WinSCP 5.21.5 (same on older)
W10
SFTP
GUI - Synchronize (target Remote, Mode Synchronize files, comparison time,size), preview changes

26600 folders, 107000 files (aprox 4 files per folder)
bitvise SSH server
50 mBit/s connection, low ping (czech datacenter)

1)
Load 26000 folders to panel takes about 5sec
Synchronize - Comparing takes about 12 minutes. (only hundreds of changes)
It is normal speed ? (by SFTP communication desing)

2)
after all synchonize transfer finishing (99% in dialog header)
most time program freeze and do not respond (i am wait 20+ min)
(all files transfered OK - with next comparing)

Thanks