How rows usage is actually counted?
Because I try to cross check with number of rows for each sheets. The 55,869 doesn’t make senses
Every row in every table that is referenced anywhere in your App is counted.
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Meaning the relation part?
If a table is referenced through a relation, then every row in that table is counted.
If you want to find if a table is counted, do find uses on every column in the table. If none of them are used, rows in that table won’t be counted.
what happen if i exceed the rows?
The Glide Police will knock down your door and steal your internet 
I don’t know. Some limits are enforced, and some are not. But it’s best to plan as if all limits are enforced 
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I had achieved/delete thousands of rows but rows usage remain the same .
How can i know that which rows consume the usage?
Once you identify which tables are referenced, you could do a rollup of all rows in each of those tables, then add them all together.
let say we have 5 rows and 5 columns used.
then, it will be counted as 25 or 5?
and another question is if Table 1 we have 10 columns and 10 rows, Table 2 have 15 rows and 16 columns and both table relate to each other. how its counted?
Update: According to your statement:
2nd scenario will counted as 10x15 isn’t?
Columns aren’t counted, only rows.
You could have 5 rows and 1 million columns, and that’s still just 5 rows.
Table 1: 10 rows
Table 2: 15 rows
Total: 25 rows
The relations make no difference. Each row is only counted once.
Can i do checking something like this?
Check each table, as last row number and add for each sheet?
Another question, how much the time taken for them to update in “usage” page after the update made?
Yes, you could do that.
That should tell you the maximum number of rows used (there could be some tables that aren’t referenced, which would reduce the count).
I don’t know about that. I think updates are almost real time, but I’m not sure about row count.
I do manually and its only takes 7,000 ++ rows.
How 
Yes, that’s quite a big difference.
If you’re sure you haven’t missed anything, then probably the best thing to do is submit a ticket with Glide Support. You can do that via Settings → Support.
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Try deleting all empty rows from all tables, check if they return, and if yes, identify which formula (specifically arrayformula) might be causing it.
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