The .SQLITE model database file is extremely large, even for a model with a reasonable number of elements and alternatives. For example 6 GB for a 7000 pipe model. This may make performance very sluggish and take a long time to open and save.
First, try compacting the database and purging records to save space, in case old records of previously removed elements and components are still stored in the database. This is done by opening the product without opening any models, then going to File > Database Utilities > Compact Database > Select Model > choose the Purge option.
If compacting the database does not help, This issue has been known to occur when the Change Tracking feature has been turned on and the user has performed bulk operations such as ModelBuilder imports and automated design runs. These types of operations can result in a large number of extra rows of data in the change tracking system (sometimes tens of millions of rows). A future version may include enhancements to avoid this problem or prompt (reference PBI # 136596), but in the meantime, if you find that the Change Tracking feature (under the Review menu) contains a very large amount of data, please contact Technical Support (for example post in the Forum) to manually remove the information from the database, or use the below advanced change tracking cleanup steps.
Note: the following information is for advanced users who are comfortable with directly editing the model database. Care should be taken to back up your model before performing these steps. If in doubt, contact Technical Support.
Using Change Tracking
Compacting a database for optimal performance and general troubleshooting