Please ignore my earlier post.
Some of potential legal arguments:
A. 'Due Date' of filing return u/s 39(1) for the period from July, 17 to Mar, 19 is not yet lapsed considering various notifications issued in those period which is extended time-limit to file return u/s 39 (1) (For examples: Notification No. 58/2017-Central Tax, dated 15th November, 2017, Notification No. 44/2018-C.T., dated 10-9-2018, as amended from time to time). These notifications are not withdrawn till date.
A1. Thus, there is no delay by your client in filing returns in Form GSTR-3B for the period from June, 2018 to March, 2019.
B. As per Section 39(10), a registered person is not be allowed to furnish a return for a tax period if the return for any of the previous tax periods has not been furnished by him.
B1. As due date of filing returns for period till March, 2019 is still not lapsed, due date of filing return for Sept, 2019 - for the purpose of Section 16(4) - cannot be earlier than 'actual date of filing returns by your client for the period till March, 2019'.
B2. Due date of filing annual return for FY 2018-19 was 31.03.2020 and your client must have filed it (if applicable) after 'filing form GSTR-3B/s for Jun, 18 to Mar, 19 in January, 2020'.
B3. In view of above, ITC for the period from June, 2018 to March, 2019 is taken by your client within the time-limit permitted u/s 16(4).
Please note that these arguments should not be taken as my views / opinion per se. But same are just some line of argument/s if you want to contest the demand. As jurisprudence of GST law is at nascent stage and still evolving, these arguments will be thoroughly tested in courts of law over a period in future.
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.