I don't think the smartlist is "damaged". From what you say the smartlist runs correctly and collects the rows of data up to the maximum number of records you set in the search criteria.
I have known in the past that issues with the data itself can cause these sorts of problems - in so far as, if some records are "incomplete" or "damaged", it interrupts the process that the system is trying to perform when it works through all the necessary transaction records.
It may be worth trying the following - perhaps in the TEST company to start with - and if you do it in the LIVE company, take a SQL backup of the live company first!
You should also get the other Dynamics Users logged out from the Dynamics system.
Press the Microsoft Dynamics GP button then select Maintenance > Check Links
In the "Check Links" window, select series "Purchasing" and then from the list of Logical Tables on the left hand side, select "Purchasing Transactions" and then click the Insert button to place it into the Selected Tables list on the right hand side.
Then press the OK button.
The Report Destination window will then pop-up. You would certainly want to display the results to screen but I suggest you might want to print a copy also. Then press OK.
The system will then perform a records check routine on the POP transactions and when finished, it will show a "File Maintenance Error Report" to screen. This will show any issues it has found and what it has done about them.
The routine may take some minutes to run - so be patient and let it get to the end(!)
[The end will be when you see the report on screen]
If the routine has adjusted/corrected records, try your smartlist again and see if there is any change in the result.
