There are two different settings which control the number of assets that will be indexed in an Index Block:
Max Rendered Assets - this option is found in the Edit interface for Index Blocks
Max Assets in Index Blocks - this option is found in Administration > Preferences > Content > Index Blocks
When an Index Block stops indexing assets, one of these limits has likely been reached.
If the Max Rendered Assets option is already set to 0 (unlimited), the Max Assets in Index Blocks setting (which is global) could be set to a value which is lower than the Max Rendered Assets setting in the Index Block.
To see if this is the case, temporarily change the Max Assets in Index Blocks field to 0 (which indicates 'unlimited'). Then, check to see whether or not the remaining assets appear in the Index Block output.
NOTE: It is recommended that both of the settings mentioned above are set to a finite number. Having an unlimited number of assets returned in Index Blocks can decrease performance in systems with a very large number of assets.