Hello!
It seems that there is a performance issue in SQLite. In some cases (index by function + "and" in 'where' condition) index is not used in a 'where' clause.
Initially the issue was reproduced only for queries that consist of more than 1 tables (join, etc..).
However, starting from version 3.36 (to be exact from rev. b775c976822b1951506bf01c8cc6b223ba079627) the issue spread to selects from single table.

Simple example, "abs()" can be replaced with any function:

CREATE TABLE "test1" (
    "Id"    INTEGER NOT NULL,
    "value"    INTEGER,
    PRIMARY KEY("Id" AUTOINCREMENT)
);
CREATE INDEX "test1_abs_value_index" ON "test1" ( abs(value) );

Lets compare results of different SQLite versions:
1. version 3.35
   EXPLAIN QUERY PLAN select * from test1 where abs(value) = abs(1) and value = 1;
   `--SEARCH TABLE test1 USING INDEX test1_abs_value_index (<expr>=?)

2. version 3.36
   EXPLAIN QUERY PLAN select * from test1 where abs(value) = abs(1) and value = 1;
   `--SCAN test1 

Using similar example with join clause shows that bug exists on any SQLite version:

CREATE TABLE IF NOT EXISTS "test2" ("Id"  INTEGER NOT NULL,  PRIMARY KEY("Id" AUTOINCREMENT));
CREATE TABLE IF NOT EXISTS "test1" (
    "Id"    INTEGER NOT NULL,
    "value"    INTEGER,
    PRIMARY KEY("Id" AUTOINCREMENT)
);
CREATE INDEX IF NOT EXISTS "test1_abs_value_index" ON "test1" ( abs(value) );

1. EXPLAIN QUERY PLAN select * from test1 join test2 on test1.id=test2.id where abs(value) = abs(1);
  |--SEARCH TABLE test1 USING INDEX test1_abs_value_index (<expr>=?)
  `--SEARCH TABLE test2 USING INTEGER PRIMARY KEY (rowid=?)

2. EXPLAIN QUERY PLAN select * from test1 join test2 on test1.id=test2.id where abs(value) = abs(1) and value=1;
  |--SCAN TABLE test1
  `--SEARCH TABLE test2 USING INTEGER PRIMARY KEY (rowid=?)

The issue appeared in propagateConstants() method, that is one of optimizations, but seems to change expression tree in some "incorrect" way.
There were changes on the revision b775c976822b1951506bf01c8cc6b223ba079627 that weaker condition (removed pTabList->nSrc>1)
so the propagateConstants() called for selects from single table.