I’m not familiar with the import but it doesn’t look too complicated from looking at one of those files.
In your first post you said that it inserted 1406 for the number of repeater rows. The two items involved would be
<trans-unit resname="field-subpages-0" restype="string" datatype="html" id="field-subpages-0">
<source><![CDATA[4]]></source>
<target><![CDATA[4]]></target>
</trans-unit>
and
<trans-unit resname="field-subpages_3_subpage-0" restype="string" datatype="html" id="field-subpages_3_subpage-0">
<source><![CDATA[1406]]></source>
<target><![CDATA[1406]]></target>
</trans-unit>
The second one is the last row to be inserted. The only reason that I can see that this would happen is that the import is ignoring everything after field-subpages on the row content.
Honestly, I don’t see why they say the import is not compatible with ACF, if all the content is inserted into the fields it’s supposed to be inserted into there should be no reason why it wouldn’t work. What if you just had custom fields with the same names? Example, if you created a field named my_test_field and another field named my_test_field_0_xxxx not using acf would it confuse those field names as well?
