Writing directly in SQL tables

Hi experts,
We have an external application which creates records directly in sql nav tables (I know is highly not recommended).
If I do a run or a COUNT from NAV, I see less records than directly in the sql. (The property DataPerCompany is YES)
Is this normal?? Do you know how can I solve this issue??

(I know that we've to use web services instead of that and we're doing it, but it takes time...)

My client is in NAV 2016, I didn't have this problem with the previous versions. Does Microsoft changed something regarding this??? Any piece of advice??

Thanks

Gonzalo