The Magic Flute solution
by Kegler

As suggested by 26 Across, THE PIED PIPER, a “RAT” has been removed from each of fifteen entries.

The Magic Flute solution grid

Across
1P + ROBE
5R(ATHE)R (HEAT anag)
8COAL ("COLE" hom)
12M(O)IET + Y (TIME anag)
14ER(RAT)A
15E + RNS
16SE(G)AL
17CELEBRATES (BEETLE CARS anag)
19BER + ATES (REB rev; EAST anag)
20S + HOT
22SE(T)H
25ORATED (TO DEAR anag)
26THE PIED PIPER
29L(I + QUID + DIE)T
31WAL(NU)T
32R(A + TIme)ON'S
33AN(I + SEE)D
36ORGAN (ORANG anag)
39NARRATES (rev hidden)
41R(A + D)IUM (MUIR rev)
42AND + ROID (rev)
43O + PEN
44NA(K)ED (DEAN rev)
45CAST + RATING
Down
1P(IR)ATES
2O + SAGES
3B + REASTPIN (PAINTERS anag)
4EAR(L)S
5H + ON + CHO
6EMS (odd letters)
7ROLLTOP (TROLLOP anag)
8CITRATES (IT REACTS anag)
9ATM (1st letters, &lit)
10LYRATE (REALTY anag)
11BREECH ("BREACH" hom)
13EM + BED (ME rev)
18SHOR(TEN)ING
19BOy + T(SWAN)AN
21gOLDIE
23T(R)EES
24PRATIQUE (QUIT PER A anag)
27PRA[T/y]ING
28BAN + AN + A
30DI(OD)ES
34SERRA + TE
35ERRAT(I)C (CRATER anag)
37R(I)OT
38AMEN (NAME anag)
40SOD (rev)