Hi toging, your 24 months begins from FLR validity.
The earliest you may apply for ILR is 28 days before the end of the 24 month living in UK period.
Why do you think you cannot visit Philippines during that time?
FLR does not prevent you from travelling.
BTW may I suggest you take a look at the ILR form as there are some conditions that you need to prepare for right now. Such as documents/letters spread over the 24 months period to prove co-habitation.
Hope that helps you in you Philippines visit preparations.