I am very close to the ILR mark but I have my insecurities

My life in UK to date: (No gaps)
Tier 4 Entry date 17th August 2008-2012
Tier 2 2013 - March 2018 (Lost my sponsor - Long story)
Applied for FLR (FP - Established life based on the 10 year route) on 28th March 2018 - Decision on it is pending

Please note, I do not have a partner. I applied for FP based on my established life and personal circumstances. The latter is fairly serious at least to me but I do not know how HO are going to perceive them.
The earliest date for ILR for me is 21st July 2018

(Have I counted this right: 17th August - 28 days = 21st July 2018?) Please do let me know, if my count is right or wrong here).

I also want to know, what happens if the UKVI does make a decision in the next week or two?
The following seem to be relevant:
39E. This paragraph applies where
(1) the application was made within 14 days of the applicant’s leave expiring and the Secretary of State considers that there was a good reason beyond the control of the applicant or their representative, provided in or with the application, why the application could not be made in-time; or
(2) the application was made:
(a) following the refusal of a previous application for leave which was made in-time or to which sub-paragraph (1) applied; and
(b) within 14 days of:
(i) the refusal of the previous application for leave; or
(ii) the expiry of any leave extended by section 3C of the Immigration Act 1971; or
(iii) the expiry of the time-limit for making an in-time application for administrative review or appeal (where applicable); or
(iv) any administrative review or appeal being concluded, withdrawn or abandoned or lapsing.
Is there a similar 14 day period, if God forbidden my application becomes invalid? I have sent quiet a few copies as my documents but kept the originals for my ILR application. The passport, BRP and a couple of other documents were original though.
I gave my biometrics on 14th May 2018.
Oh and if I am varying my application to ILR, am I going to get my money back of £1033? I am actually planning to pay: ILR fee - £1033 for the variation (I am planning to clarify this on the cover letter) Is that acceptable?
Also, which premium phone number am I supposed to call to confirm the variation? I do not want my FLR (FP) to be refused after the 21st, in case, the UKVI is unaware of the second application.
All your answers/advice (negative or positive) are most welcome!
