A little more difficult than some EVs, with one or two clues holding me up for a short while and one quibble at 31d. I’m not sure I like being given a solving strategy so I tend not to read it until after I have completed the puzzle. However it is probably useful for those new to barred-grid puzzles.
What needed to be done to clues was clear from the preamble, though on first reading it seemed to indicate that all clues were affected rather than just five. However, this misconception was soon corrected after solving the first couple of clues.
For the unclued answers I have shown the interpretation and the clue affected.
*(XXX) – anagram
[x] – letter(s) removed/unused
Across
1 SPARKS PARK (to stop) in SS (on board)
6 SUMMERset SUMMER (totter) set (apparatus) – set off (depart) – 38a
11 OPEN OP (out of print) EN (printing unit)
12 OISE [p]OISE (carriage losing power)
13 RE-ENTER RE[s]ENTER (bitter persons not succeeded)
15 IMIDE MID (junior officer) in IE (that is)
16 NEURITE NE (not, obsolete) IT in URE (use, historically)
20 beSIDES [ash]eS in bIDES (remains) – be off (scat) – 34d
21 ATTENTAT AT (visiting) TENT (shelter) A T (tense)
22 SlashING shIN (part of leg) in SlaG(scum) – lash out (spend) – 5d
24 LAIR – hideout – 28a
25 TOP-LEVEL [pe]OPLE in TV [chann]EL
28 BRERE RE (about) in BR (branch) [grov]E
30 OTRANTO [m]O[a]T RAN TO (was sufficient)
32 PARSI PARS[ing] (most of the explanation of Latin) I
35 SOUROCK OUR in SOCK (Argyle say)
36 NORI NOR I (me neither)
37 EILD LIE (story) reversed D (date)
38 DEPART – set off – 6a
39 SCEATT E (European) in SCATT[y] (mostly disorganised)
Down
1 SHRINAL SHRI (title of respect) AN (one) reversed L (line)
2 POEM – Paradise Lost – 29d
3 AGEIST A GEIST (dominant principle)
4 RAND R AND [a] (golf club)
5 SPEND – lash out – 22a
6 SERENA REN[d] (tear not fully) in SEA (main)
7 UNJUSTLY UN (a, in French) ST (holy man) in JULY (summer month)
8 MORRISES MOR (East Anglican girl) RISES (comes to prominence)
9 MIDI I (one) DIM (not hopeful) reversed
10 REDES SEDER (Jewish ritual) reversed
14 CTENES C[ondui]T *(SEEN)
17 STARTS ST (stone) ARTS (sculpture and other similar things)
18 TERRARIA ERR (mistake) in T[annhauser] ARIA (melody)
19 INTENDER [tra]IN TENDER (old railway carriage)
23 GLAIKET LAIK (to skive up North) in GET (child
26 OUTSIT OU (where, in French) [nut]S in TIT (bird)
27 VERONA V (see) A N (new) ORE (mineral) reversed
28 hideBOUND i (one) deB (fashionable girl) in hOUND (obstinate scoundrel) – hideout (lair) – 24a
29 FOOLS paradise *(aSsaiLed prOOF) – Paradise Lost (poem) – 2d
31 RURP R (right) in PUR ( run) reversed – pur or purr is the sound of an engine etc running not ‘run’
33 ARLE hidden in ‘regulAR LEssons’
34 SCAT – be off – 20a