Not sure if this will help your particular issue but I have not experienced
any issues with QIF files when moving from GnuCash v2 to v3.
I am, however, using MoneyManagerEx for Android to export .qif files and
that has not changed in the meantime. 
You should be able to open the generated .qif file in any text editor and
compare to another one to try to identify any issues.
Some references I've collected while writing the QIF export module, can be
found here:
https://github.com/moneymanagerex/android-money-manager-ex/issues/211



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