There could be a potential thawing of relations between the Philippines and Taiwan this 2016, given the fact that both countries held presidential elections, won by Rodrigo Duterte and Tsai Ing-wen, respectively, and the overall situation in the region which was marked by increased Chinese activity in the South China Sea/West Philippine Sea, thus straining relations with practically all countries surrounding the said body of water, including the Philippines which filed an arbitration case in the International Tribunal for the Law of the Sea (ITLOS).
(READ: http://tankler.com/taiwan-president-wants-to-prioritize-good-relation-to-philippines-6181)
There are certain issues hampering the growth of relations between the two, such as an overlapping EEZ (which has resulted with a fatal shooting incident in 2013 which resulted in tensions which have since subsided and efforts have been made to settle disputes.
(For your reference, read these links: http://www.philstar.com/headlines/2015/11/19/1523686/philippines-signs-fishing-agreement-taiwan
http://www.asianews.network/content/taiwan-philippines-sign-marine-patrol-cooperation-pact-4049)
Manila and Taipei has maintained informal economic and cultural ties, however, with the present situation in foreign relations, there should be much caution, and let’s just all hope for the best (that is, the ITLOS will eventually side with our case thus giving us more leverage in negotiating with China).