This was fun to write, but its a hack and a half. Not sure it meets your exact requirements , but hopefully give you some ideas. You probably want to write a script in Python or something to do this properly.

Note: I'm using Linux, you will need alter path names ('/tmp/run.sql' for this to work on other platforms).

Create two scripts:

• script1.sql
• script2.sql

For instance:

-- script1
-- This will populate the tables based on the flat table.
-- Then drop the flat table
-- Do whatever here
DROP TABLE flat;

-- script2
-- This will create the flat table and populate from relational tables
CREATE TABLE flat(n); -- dummy table
-- Whatever

Open up your DB; and store them in the sqlar table. This is optional - you could just use external files, but this way you get to ship them all wrapped-up nice and cosy in the database itself.

$ sqlite3 hack.db
SQLite version 3.31.1 2020-01-27 19:55:54
Enter ".help" for usage hints.
sqlite> .archive --create
sqlite> .archive --insert script1.sql
sqlite> .archive --insert script2.sql

To extract a particular file to a new location, we may need to decompress the contents. The function sqlar_uncompress will take care of this for us.

sqlite> select writefile('/tmp/run.sql',sqlar_uncompress(data,sz)) as size_written
   ...> from sqlar where name='script1.sql';
size_written
131

To write the contents conditionally; we'll need to check for the existence of the table called 'flat'. Use the sqlite_schema table to look for it. Note I'm using the older synonym for this table as I happen to on an older version of sqlite3 at the moment.

sqlite> create table if not exists flat(n);
sqlite> select * from sqlite_master where (name,type)==('flat','table');
type|name|tbl_name|rootpage|sql
table|flat|flat|4|CREATE TABLE flat(n)

sqlite> drop table if exists flat;
sqlite> select * from sqlite_master where (name,type)==('flat','table');
sqlite> 

Note: the 'if not exists' and 'exists' conditions only apply to the DDL in question, so they can't be used (I don't think?) for other conditional statements. They just make the examples more illustrative.

Put it together: we can now conditionally write out different SQL out to a file based on whether a table exists.

So - to output 'script1.sql' if 'flat' exists:

sqlite> create table if not exists flat(n);
sqlite> select writefile('/tmp/run.sql',sqlar_uncompress(data,sz)) as o
   ...> from sqlar ar
   ...> join sqlite_master s on (s.name,s.type)==('flat','table')
   ...> where ar.name='script1.sql';
o
131
sqlite> .shell cat /tmp/run.sql
-- This will populate the tables based on the flat table.
-- Then drop the flat table

-- Do whatever here

DROP TABLE flat;
sqlite> 

The same thing, but this time 'flat' doesn't exist:

sqlite> drop table flat;
sqlite> select writefile('/tmp/run.sql',sqlar_uncompress(data,sz)) as o
   ...> from sqlar ar
   ...> join sqlite_master s on (s.name,s.type)==('flat','table')
   ...> where ar.name='script1.sql';

And to write out 'script2' only if 'flat' does NOT exist:

sqlite> create table if not exists flat(n);
sqlite> select writefile('/tmp/run.sql',sqlar_uncompress(data,sz)) as o
   ...> from sqlar ar
   ...> where ar.name='script2.sql'
   ...> and not exists (select 1 FROM sqlite_master s where (s.name,s.type)==('flat','table'));
sqlite> 

Same thing, but this time flat does not exist:

sqlite> drop table if exists flat;
sqlite> select writefile('/tmp/run.sql',sqlar_uncompress(data,sz)) as o
   ...> from sqlar ar
   ...> where ar.name='script2.sql'
   ...> and not exists (select 1 FROM sqlite_master s where (s.name,s.type)==('flat','table'));
o
120

Lastly: use '.read' to run whatever is in the output file 'run.sql'.

sqlite> .shell rm -rf /tmp/run.sql
sqlite> create table if not exists flat(n);
sqlite> .tables
flat   sqlar
sqlite> 
sqlite> select writefile('/tmp/run.sql',sqlar_uncompress(data,sz)) as o
   ...> from sqlar ar
   ...> join sqlite_master s on (s.name,s.type)==('flat','table')
   ...> where ar.name='script1.sql';
o
131
sqlite> 
sqlite> select writefile('/tmp/run.sql',sqlar_uncompress(data,sz)) as o
   ...> from sqlar ar
   ...> where ar.name='script2.sql'
   ...> and not exists (select 1 FROM sqlite_master s where (s.name,s.type)==('flat','table'));
sqlite> 
sqlite> .read /tmp/run.sql
sqlite> .tables
sqlar

Then just running the same SQL again:

sqlite> select writefile('/tmp/run.sql',sqlar_uncompress(data,sz)) as o
   ...> from sqlar ar
   ...> join sqlite_master s on (s.name,s.type)==('flat','table')
   ...> where ar.name='script1.sql';
sqlite> 
sqlite> select writefile('/tmp/run.sql',sqlar_uncompress(data,sz)) as o
   ...> from sqlar ar
   ...> where ar.name='script2.sql'
   ...> and not exists (select 1 FROM sqlite_master s where (s.name,s.type)==('flat','table'));
o
131
sqlite> 
sqlite> .read /tmp/run.sql
sqlite> .tables
flat   sqlar

Here's the script source without the sqlite prompt etc:

.shell rm -rf /tmp/run.sql
.tables

select writefile('/tmp/run.sql',sqlar_uncompress(data,sz)) as o
from sqlar ar
join sqlite_master s on (s.name,s.type)==('flat','table')
where ar.name='script1.sql';

select writefile('/tmp/run.sql',sqlar_uncompress(data,sz)) as o
from sqlar ar
where ar.name='script2.sql'
and not exists (select 1 FROM sqlite_master s where (s.name,s.type)==('flat','table'));

.read /tmp/run.sql
.tables